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PDB | 3KOJ | Crystal structure of the SSB domain of Q5N255_SYNP6 protein from Synechococcus sp. Northeast Structural Genomics ...

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Internal ID
69040
PDB Entry ID
3KOJ
Title
Crystal structure of the SSB domain of Q5N255_SYNP6 protein from Synechococcus sp. Northeast Structural Genomics Consortium Target SnR59a.
Authors
Vorobiev, S.,Su, M.,Seetharaman, J.,Wang, H.,Foote, L.E.,Ciccosanti, C.,Janjua, H.,Xiao, R.,Acton, T.B.,Montelione, G.T.,Tong, L.,Hunt, J.F.,Northeast Structural Genomics Consortium (NESG)
Primary Citation
AuthorsVorobiev, S., Su, M., Seetharaman, J., Wang, H., Foote, L.E., Ciccosanti, C., Janjua, H., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.
TitleCrystal structure of the SSB domain of Q5N255_SYNP6 protein from Synechococcus sp.
JournalTo be Published
AbstractView
 
History
Deposition: 2009-11-13Release: 2009-11-24Last Modified:
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.890.2020.2010.218C 2 2 21
Unit Cell
Length [Å]a70.84b113.03c73.38
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1uncharacterized protein ycf41T19ASSB domainA, B
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Synechococcus elongatus PCC 6301Anacystis nidulansEscherichia coli BL21(DE3)
Chemical Component
IdentifierNameFromulaLigand StructureLigand Interaction
MSESELENOMETHIONINEC5H11NO2Se[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordDNA BINDING PROTEIN
Textsingle-strand binding protein family, PF00436, SNR59A, NESG, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, DNA-binding, DNA BINDING PROTEIN
 
Polymeric Molecules
Chain A
Descriptionuncharacterized protein ycf41
FragmentSSB domain
MutationT19A
Polymer typepolypeptide
Formula Weight12345.7
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain B
Descriptionuncharacterized protein ycf41
FragmentSSB domain
MutationT19A
Polymer typepolypeptide
Formula Weight12345.7
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anoyesn/aA,Bpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
MSESELENOMETHIONINEC5H11NO2Se196.107View
Natural/Genetically Modified Source
Common NameAnacystis nidulans
Scientific NameSynechococcus elongatus PCC 6301
Source Genusn/a
Genesyc1425_d, ycf41
Host Common Namen/a
Host Scientific NameEscherichia coli BL21(DE3)
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)+ Magic
Host Vector Typeplasmid
Host PlasmidpET 14-15C
 
Crystallization Experiments
MethodMicrobutch under parafin oil
PH7.5
Temperature291.0
Details4M sodium chloride, 0.1M HEPES pH 7.5 , Microbutch under parafin oil, temperature 291K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
70.84113.0373.38
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
C 2 2 21
Diffraction Detector
DetectorCCD
TypeADSC QUANTUM 4
Detailsn/a
Collection Date2009-11-11
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.97903
 
Diffraction Source
SourceSYNCHROTRON
TypeNSLS BEAMLINE X4A
SiteNSLS
BeamlineX4A
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)1.89
Resolution (Low)50.00
Number Reflections (All) 45223
Number Reflections (Observed)44952
Percent Possible (Observed)99.4
R Merge I (Observed)0.105
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy7.0
 
High Resolution Shell Details
Resolution(High)1.90
Resolution(Low)1.97
Percent Possible(All) 97.00
R Merge I(Observed)0.666
Mean I Over Sigma(Observed)2.7
R Sym I(Observed)n/a
Redundancy6.1
Num Unique Reflections(All)4508
 
Refinement Statistics
Structure Solution MethodSAD
Resolution (High)1.89
Resolution (Low)36.69
Cut-off Sigma (F)1.0
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)44926
Number of Reflections (R-Free) 2292
Percent Reflections (Observed)99.32
R-Factor (All)n/a
R-Factor (Observed)0.202
R-Work0.2011
R-Free0.2183
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Valuen/a
Anisotropic B[1][1]n/a
Anisotropic B[1][2]n/a
Anisotropic B[1][3]n/a
Anisotropic B[2][2]n/a
Anisotropic B[2][3]n/a
Anisotropic B[3][3]n/a
 
Resolution Shells
Shell Resol (High)1.89
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)156
Number of Reflections (R-Work)2489
R-Factor (R-Work)0.255
R-Factor (R-Free)0.246
R-Free Errorn/a
Percent Reflections (Observed)94.00
 
Shell Resol (High)1.94
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)136
Number of Reflections (R-Work)2683
R-Factor (R-Work)0.219
R-Factor (R-Free)0.265
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)1.98
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)137
Number of Reflections (R-Work)2703
R-Factor (R-Work)0.213
R-Factor (R-Free)0.221
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.03
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)131
Number of Reflections (R-Work)2701
R-Factor (R-Work)0.208
R-Factor (R-Free)0.229
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.09
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)140
Number of Reflections (R-Work)2687
R-Factor (R-Work)0.202
R-Factor (R-Free)0.249
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.15
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)150
Number of Reflections (R-Work)2682
R-Factor (R-Work)0.194
R-Factor (R-Free)0.204
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.22
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)132
Number of Reflections (R-Work)2690
R-Factor (R-Work)0.188
R-Factor (R-Free)0.270
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.30
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)166
Number of Reflections (R-Work)2642
R-Factor (R-Work)0.181
R-Factor (R-Free)0.184
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.39
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)148
Number of Reflections (R-Work)2667
R-Factor (R-Work)0.194
R-Factor (R-Free)0.251
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.50
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)141
Number of Reflections (R-Work)2705
R-Factor (R-Work)0.204
R-Factor (R-Free)0.191
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.63
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)129
Number of Reflections (R-Work)2675
R-Factor (R-Work)0.224
R-Factor (R-Free)0.227
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)2.79
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)163
Number of Reflections (R-Work)2685
R-Factor (R-Work)0.227
R-Factor (R-Free)0.215
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)3.01
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)130
Number of Reflections (R-Work)2696
R-Factor (R-Work)0.207
R-Factor (R-Free)0.244
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)3.31
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)149
Number of Reflections (R-Work)2662
R-Factor (R-Work)0.176
R-Factor (R-Free)0.199
R-Free Errorn/a
Percent Reflections (Observed)100.00
 
Shell Resol (High)3.79
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)151
Number of Reflections (R-Work)2664
R-Factor (R-Work)0.161
R-Factor (R-Free)0.179
R-Free Errorn/a
Percent Reflections (Observed)99.00
 
Shell Resol (High)4.77
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)133
Number of Reflections (R-Work)2603
R-Factor (R-Work)0.222
R-Factor (R-Free)0.218
R-Free Errorn/a
Percent Reflections (Observed)97.00
 
RMS Deviations
Parameter TypeDeviation From Ideal
f_bond_d0.043
f_angle_d1.582
f_dihedral_angle_d17.803
f_chiral_restr0.106
f_plane_restr0.013
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms1388
Nucleic Acid Atoms0
Heterogen Atoms0
Solvent Atoms182
 
Programs
Data CollectionHKL-2000
Data Reduction (intensity integration)DENZO
Data Reduction (data scaling)SCALEPACK
Structure SolutionBnP, PHENIX(phenix.autosol; phenix.autobuild)
Structure RefinementPHENIX (phenix.refine: 1.5_2)
 
Software
Classificationdata collection
Software NameHKL-2000
 
Classificationmodel building
Software NameBnP
 
Classificationmodel building
Software NamePHENIX(phenix.autosol
 
Classificationmodel building
Software Namephenix.autobuild)
 
Classificationrefinement
Software NamePHENIX
Software Version (phenix.refine: 1.5_2)
 
Sequence Chain
A
Sequence
  1   MGHHHHHHSH  MNSCILQATV  VEAPQLRYAQ  DNQTPVAEMV  VQFPGLSSKD  APARLKVVGW

 61   GAVAQELQDR  CRLNDEVVLE  GRLRINSLLK  PDGNREKQTE  LTVTRVHH  

Sequence Chain
B
Sequence
  1   MGHHHHHHSH  MNSCILQATV  VEAPQLRYAQ  DNQTPVAEMV  VQFPGLSSKD  APARLKVVGW

 61   GAVAQELQDR  CRLNDEVVLE  GRLRINSLLK  PDGNREKQTE  LTVTRVHH