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PDB | 3FZV | Crystal structure of PA01 protein, putative LysR family transcriptional regulator from Pseudomonas aeruginosa

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Internal ID
64196
PDB Entry ID
3FZV
Title
Crystal structure of PA01 protein, putative LysR family transcriptional regulator from Pseudomonas aeruginosa
Authors
Knapik, A.A.,Tkaczuk, K.L.,Chruszcz, M.,Wang, S.,Zimmerman, M.D.,Cymborowski, M.,Skarina, T.,Kagan, O.,Savchenko, A.,Edwards, A.M.,Joachimiak, A.,Bujnicki, J.M.,Minor, W.,Midwest Center for Structural Genomics (MCSG)
Primary Citation
AuthorsKnapik, A.A., Tkaczuk, K.L., Chruszcz, M., Wang, S., Zimmerman, M.D., Cymborowski, M., Skarina, T., Kagan, O., Savchenko, A., Edwards, A.M., Joachimiak, A., Bujnicki, J.M., Minor, W.
TitleCrystal structure of PA01 protein, putative LysR family transcriptional regulator from Pseudomonas aeruginosa
JournalTo be Published
AbstractView
 
History
Deposition: 2009-01-26Release: 2009-03-10Last Modified: 2011-07-13
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.710.2270.2240.279P 1 21 1
Unit Cell
Length [Å]a54.33b155.06c72.44
Angles [°]alpha90.00beta92.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Probable transcriptional regulatorA, B, C, D
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Pseudomonas aeruginosa PA01Escherichia coli
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
MSESELENOMETHIONINEC5H11NO2Se[View][View]
SO4SULFATE IONO4S2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTRANSCRIPTION REGULATOR
TextLysR, transcriptional regulator, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, DNA-binding, Transcription, Transcription regulation, TRANSCRIPTION REGULATOR
 
Polymeric Molecules
Chain A
DescriptionProbable transcriptional regulator
Polymer typepolypeptide
Formula Weight34385.6
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain B
DescriptionProbable transcriptional regulator
Polymer typepolypeptide
Formula Weight34385.6
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain C
DescriptionProbable transcriptional regulator
Polymer typepolypeptide
Formula Weight34385.6
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain D
DescriptionProbable transcriptional regulator
Polymer typepolypeptide
Formula Weight34385.6
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anoyesn/aA,B,C,Dpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
MSESELENOMETHIONINEC5H11NO2Se196.107View
SO4SULFATE IONO4S296.058View
Natural/Genetically Modified Source
Scientific NamePseudomonas aeruginosa PA01
Source Genusn/a
GenePA0218
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)Codon Plus RIPL
Host Vector Typeplasmid
Host PlasmidpMCSG7
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH5.5
Temperature293.0
Details25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
54.33155.0672.44
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0092.0090.00
Space Group
P 1 21 1
Diffraction Detector
DetectorCCD
TypeADSC QUANTUM 315
Detailsmirrors
Collection Date2008-02-24
 
Diffraction Radiation
MonochromatorSi(111) CHANNEL
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.9794
 
Diffraction Source
SourceSYNCHROTRON
TypeAPS BEAMLINE 19-ID
SiteAPS
Beamline19-ID
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)-3.0
Resolution (High)2.70
Resolution (Low)50.00
Number Reflections (All) 32197
Number Reflections (Observed)32197
Percent Possible (Observed)99.1
R Merge I (Observed)0.090
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy4.9
 
High Resolution Shell Details
Resolution(High)2.70
Resolution(Low)2.75
Percent Possible(All) 98.50
R Merge I(Observed)0.569
Mean I Over Sigma(Observed)2.8
R Sym I(Observed)0.569
Redundancy5.0
Num Unique Reflections(All)1563
 
Refinement Statistics
Structure Solution MethodSAD
Resolution (High)2.71
Resolution (Low)50.00
Cut-off Sigma (F)0.0
Cut-off Sigma (I)0.0
Number of Reflections (All)30555
Number of Reflections (Observed)30555
Number of Reflections (R-Free) 1627
Percent Reflections (Observed)98.85
R-Factor (All)0.22712
R-Factor (Observed)0.22712
R-Work0.22435
R-Free0.27899
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value26.896
Anisotropic B[1][1]1.06
Anisotropic B[1][2]0.00
Anisotropic B[1][3]-0.80
Anisotropic B[2][2]-0.76
Anisotropic B[2][3]0.00
Anisotropic B[3][3]-0.36
 
Resolution Shells
Shell Resol (High)2.71
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)109
Number of Reflections (R-Work)2153
R-Factor (R-Work)0.316
R-Factor (R-Free)0.444
R-Free Errorn/a
Percent Reflections (Observed)95.04
 
RMS Deviations
First|Previous|1 of 4|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.010
r_bond_other_d0.003
r_angle_refined_deg1.241
r_angle_other_deg1.522
r_dihedral_angle_1_deg5.597
r_dihedral_angle_2_deg35.037
r_dihedral_angle_3_deg17.772
r_dihedral_angle_4_deg20.643
r_chiral_restr0.061
r_gen_planes_refined0.005
First|Previous|1 of 4|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms8268
Nucleic Acid Atoms0
Heterogen Atoms10
Solvent Atoms28
 
Programs
Data CollectionHKL-3000
Data Reduction (intensity integration)HKL-3000
Data Reduction (data scaling)HKL-3000
Structure SolutionHKL-3000, SHELXD, SHELXE, RESOLVE, COOT, MLPHARE, DM, ARP/wARP, CCP4
Structure RefinementREFMAC 5.5.0062
 
Software
Classificationdata collection
Software NameHKL-3000
 
Classificationmodel building
Software NameHKL-3000
 
Classificationmodel building
Software NameSHELXD
 
Classificationmodel building
Software NameSHELXE
 
Classificationmodel building
Software NameRESOLVE
 
Classificationmodel building
Software NameCOOT
 
Classificationmodel building
Software NameMLPHARE
 
Classificationmodel building
Software NameDM
 
Classificationmodel building
Software NameARP/wARP
 
Classificationmodel building
Software NameCCP4
 
Classificationrefinement
Software NameREFMAC
Software Version 5.5.0062
 
Sequence Chain
A
Sequence
  1   MASYTLRQLK  YFVTTVECGS  VAEASRKLYI  AQPSISTAVK  GLEESFGVQL  FIRHHAQGVS

 61   LTPAGARFYR  KAQELLRMAH  EFEQNALADN  DVIAGQIDIG  CFETVAPLYL  PGLIAGFRQA

121   YPGVEIRIRD  GEQQELVQGL  TSGRFDLAFL  YEHDLDSTIE  TEPLMPPQRP  HALLPEGHRF

181   AGQAQVSLRD  LCLEPMILLD  VQPSRTYFVS  LFEELGLTPN  IAFSSPSIEM  VRGMVGQGFG

241   FSLLVTRPHS  ECTYDGKKVV  MVDLAEPVST  SGLAAAWLKR  AQLTKPARLF  VDYCREQLGK

301   LAERRH  

Sequence Chain
B
Sequence
  1   MASYTLRQLK  YFVTTVECGS  VAEASRKLYI  AQPSISTAVK  GLEESFGVQL  FIRHHAQGVS

 61   LTPAGARFYR  KAQELLRMAH  EFEQNALADN  DVIAGQIDIG  CFETVAPLYL  PGLIAGFRQA

121   YPGVEIRIRD  GEQQELVQGL  TSGRFDLAFL  YEHDLDSTIE  TEPLMPPQRP  HALLPEGHRF

181   AGQAQVSLRD  LCLEPMILLD  VQPSRTYFVS  LFEELGLTPN  IAFSSPSIEM  VRGMVGQGFG

241   FSLLVTRPHS  ECTYDGKKVV  MVDLAEPVST  SGLAAAWLKR  AQLTKPARLF  VDYCREQLGK

301   LAERRH  

Sequence Chain
C
Sequence
  1   MASYTLRQLK  YFVTTVECGS  VAEASRKLYI  AQPSISTAVK  GLEESFGVQL  FIRHHAQGVS

 61   LTPAGARFYR  KAQELLRMAH  EFEQNALADN  DVIAGQIDIG  CFETVAPLYL  PGLIAGFRQA

121   YPGVEIRIRD  GEQQELVQGL  TSGRFDLAFL  YEHDLDSTIE  TEPLMPPQRP  HALLPEGHRF

181   AGQAQVSLRD  LCLEPMILLD  VQPSRTYFVS  LFEELGLTPN  IAFSSPSIEM  VRGMVGQGFG

241   FSLLVTRPHS  ECTYDGKKVV  MVDLAEPVST  SGLAAAWLKR  AQLTKPARLF  VDYCREQLGK

301   LAERRH  

Sequence Chain
D
Sequence
  1   MASYTLRQLK  YFVTTVECGS  VAEASRKLYI  AQPSISTAVK  GLEESFGVQL  FIRHHAQGVS

 61   LTPAGARFYR  KAQELLRMAH  EFEQNALADN  DVIAGQIDIG  CFETVAPLYL  PGLIAGFRQA

121   YPGVEIRIRD  GEQQELVQGL  TSGRFDLAFL  YEHDLDSTIE  TEPLMPPQRP  HALLPEGHRF

181   AGQAQVSLRD  LCLEPMILLD  VQPSRTYFVS  LFEELGLTPN  IAFSSPSIEM  VRGMVGQGFG

241   FSLLVTRPHS  ECTYDGKKVV  MVDLAEPVST  SGLAAAWLKR  AQLTKPARLF  VDYCREQLGK

301   LAERRH