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PDB | 3NJG | K98A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.

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Internal ID
72514
PDB Entry ID
3NJG
Title
K98A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.
Authors
Osipiuk, J.,Mulligan, R.,Bargassa, M.,Collart, F.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG)
Primary Citation
AuthorsOsipiuk, J., Mulligan, R., Bargassa, M., Hamilton, J.E., Cunningham, M.A., Joachimiak, A.
TitleCharacterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.
JournalJ.Biol.Chem., v.287, pp.19452 - 19461, 2012
AbstractView
Pubmed22493430
DOI10.1074/jbc.M112.358069
 
History
Deposition: 2010-06-17Release: 2010-07-14Last Modified: 2012-10-10
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.920.1700.1680.196H 3 2
Unit Cell
Length [Å]a99.90b99.90c100.59
Angles [°]alpha90.00beta90.00gamma120.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1PeptidaseK98AN-terminal domain 1-116A
2PeptidaseC-terminal domain 117-125B
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Shewanella oneidensisEscherichia coli
2Shewanella oneidensisEscherichia coli
Related PDB Entries
SCOP Classification
CATH Classification
Structural Details
KeywordHYDROLASE
TextSTRUCTURAL GENOMICS, ASPARTIC PEPTIDASE, AUTOCATALYSIS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, HYDROLASE
 
Polymeric Molecules
Chain A
DescriptionPeptidase
FragmentN-terminal domain 1-116
MutationK98A
Polymer typepolypeptide
Formula Weight12606.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain B
DescriptionPeptidase
FragmentC-terminal domain 117-125
Polymer typepolypeptide
Formula Weight1080.2
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
2n/anonon/aBpolypeptide(L)n/a
Natural/Genetically Modified Source
Scientific NameShewanella oneidensis
Source Genusn/a
GeneSO_1698
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)
Host Vector Typeplasmid
Host PlasmidpMCSG7
 
Scientific NameShewanella oneidensis
Source Genusn/a
GeneSO_1698
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)
Host Vector Typeplasmid
Host PlasmidpMCSG7
 
Crystallization Experiments
MethodVAPOR DIFFUSION, SITTING DROP
PH4.5
Temperature291.0
Details2.5 M sodium chloride, 0.1 M acetate buffer, 0.2 M lithium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
99.9099.90100.59
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.00120.00
Space Group
H 3 2
Diffraction Detector
DetectorCCD
TypeSBC-3
Detailsn/a
Collection Date2005-11-13
 
Diffraction Radiation
Monochromatordouble crystal monochromator
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.9792
 
Diffraction Source
SourceSYNCHROTRON
TypeAPS BEAMLINE 19-BM
SiteAPS
Beamline19-BM
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)1.92
Resolution (Low)32.80
Number Reflections (All) 14934
Number Reflections (Observed)14934
Percent Possible (Observed)100.0
R Merge I (Observed)0.182
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plot33.4
Redundancy8.7
 
High Resolution Shell Details
Resolution(High)1.92
Resolution(Low)1.98
Percent Possible(All) 99.90
R Merge I(Observed)0.633
Mean I Over Sigma(Observed)2.5
R Sym I(Observed)n/a
Redundancy5.7
Num Unique Reflections(All)1215
 
Resolution(High)1.98
Resolution(Low)2.04
Percent Possible(All) 100.00
R Merge I(Observed)0.515
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy6.6
Num Unique Reflections(All)1230
 
Resolution(High)2.04
Resolution(Low)2.11
Percent Possible(All) 100.00
R Merge I(Observed)0.412
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy7.2
Num Unique Reflections(All)1240
 
Resolution(High)2.11
Resolution(Low)2.20
Percent Possible(All) 100.00
R Merge I(Observed)0.364
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy7.8
Num Unique Reflections(All)1209
 
Resolution(High)2.20
Resolution(Low)2.30
Percent Possible(All) 100.00
R Merge I(Observed)0.383
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy8.3
Num Unique Reflections(All)1239
 
Resolution(High)2.30
Resolution(Low)2.42
Percent Possible(All) 100.00
R Merge I(Observed)0.350
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy9.1
Num Unique Reflections(All)1243
 
Resolution(High)2.42
Resolution(Low)2.57
Percent Possible(All) 100.00
R Merge I(Observed)0.382
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy10.2
Num Unique Reflections(All)1256
 
Resolution(High)2.57
Resolution(Low)2.77
Percent Possible(All) 100.00
R Merge I(Observed)0.313
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy10.5
Num Unique Reflections(All)1233
 
Resolution(High)2.77
Resolution(Low)3.05
Percent Possible(All) 100.00
R Merge I(Observed)0.218
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy10.4
Num Unique Reflections(All)1243
 
Resolution(High)3.05
Resolution(Low)3.49
Percent Possible(All) 100.00
R Merge I(Observed)0.154
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy10.1
Num Unique Reflections(All)1248
 
Resolution(High)3.49
Resolution(Low)4.39
Percent Possible(All) 99.90
R Merge I(Observed)0.137
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy9.5
Num Unique Reflections(All)1262
 
Resolution(High)4.39
Resolution(Low)40.00
Percent Possible(All) 99.80
R Merge I(Observed)0.117
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy8.9
Num Unique Reflections(All)1316
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)1.92
Resolution (Low)32.80
Cut-off Sigma (F)0.0
Cut-off Sigma (I)0.0
Number of Reflections (All)14872
Number of Reflections (Observed)14872
Number of Reflections (R-Free) 752
Percent Reflections (Observed)99.55
R-Factor (All)0.1696
R-Factor (Observed)0.1696
R-Work0.1682
R-Free0.1958
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value29.239
Anisotropic B[1][1]-0.20
Anisotropic B[1][2]-0.10
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-0.20
Anisotropic B[2][3]0.00
Anisotropic B[3][3]0.30
 
Resolution Shells
Shell Resol (High)1.92
Shell Resolution (Low)n/a
Number of Reflections (Observed)1084
Number of Reflections (R-Free)64
Number of Reflections (R-Work)1020
R-Factor (R-Work)0.258
R-Factor (R-Free)0.306
R-Free Errorn/a
Percent Reflections (Observed)99.18
 
RMS Deviations
First|Previous|1 of 2|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.018
r_bond_other_d0.003
r_angle_refined_deg1.528
r_angle_other_deg0.851
r_dihedral_angle_1_deg6.165
r_dihedral_angle_2_deg41.198
r_dihedral_angle_3_deg14.479
r_dihedral_angle_4_deg19.502
r_chiral_restr0.099
r_gen_planes_refined0.006
First|Previous|1 of 2|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms894
Nucleic Acid Atoms0
Heterogen Atoms0
Solvent Atoms118
 
Programs
Data CollectionSBC-collect
Data Reduction (intensity integration)HKL-2000
Data Reduction (data scaling)HKL-2000
Structure SolutionMOLREP
Structure RefinementREFMAC 5.5.0109
 
Software
Classificationdata processing
Software NameHKL
 
Classificationmolecular replacement
Software NameMOLREP
 
Classificationrefinement
Software NameREFMAC5
Software Version 5.5.0109
 
Classificationdata extraction
Software Namepdb_extract
Software Version 3.10
 
Sequence Chain
A
Sequence
  1   SNAMFAPQGL  AQFIKVNVTL  ENGEPVFIYT  DANGQVCQGD  ITVTQAGTIT  YLLNDQTLKG

 61   LKFVGVGFVT  PFDGIIDAVT  ISSDGMLVQL  VDLDKTPGTT  AFQFVLSNTA  NTLLVLSPD

Sequence Chain
B
Sequence
1   PQIINRPQN