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- PDB-3njg: K98A mutant of SO1698 protein, an aspartic peptidase from Shewane... -

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Basic information

Entry
Database: PDB / ID: 3njg
TitleK98A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.
Components(Peptidase) x 2
KeywordsHYDROLASE / STRUCTURAL GENOMICS / ASPARTIC PEPTIDASE / AUTOCATALYSIS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyDP-EP family / DP-EP family / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / Autocatalytic aspartic peptidase
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsOsipiuk, J. / Mulligan, R. / Bargassa, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.
Authors: Osipiuk, J. / Mulligan, R. / Bargassa, M. / Hamilton, J.E. / Cunningham, M.A. / Joachimiak, A.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)13,6862
Polymers13,6862
Non-polymers00
Water2,126118
1
A: Peptidase
B: Peptidase
x 6


Theoretical massNumber of molelcules
Total (without water)82,11912
Polymers82,11912
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area20450 Å2
ΔGint-127 kcal/mol
Surface area28050 Å2
MethodPISA
2
A: Peptidase
B: Peptidase

A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,3734
Polymers27,3734
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area4970 Å2
ΔGint-29 kcal/mol
Surface area11200 Å2
MethodPISA
3
A: Peptidase
B: Peptidase

A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,3734
Polymers27,3734
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area12070 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-5 kcal/mol
Surface area6810 Å2
MethodPISA
5
A: Peptidase
x 6


Theoretical massNumber of molelcules
Total (without water)75,6376
Polymers75,6376
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area12820 Å2
ΔGint-94 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.901, 99.901, 100.589
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Peptidase


Mass: 12606.238 Da / Num. of mol.: 1 / Fragment: N-terminal domain 1-116 / Mutation: K98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGA7
#2: Protein/peptide Peptidase


Mass: 1080.217 Da / Num. of mol.: 1 / Fragment: C-terminal domain 117-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGA7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CHAIN-B PEPTIDE IS A PRODUCT OF AUTOCATALYTIC CLEAVAGE DURING CRYSTALLIZATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.5 M sodium chloride, 0.1 M acetate buffer, 0.2 M lithium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 13, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→32.8 Å / Num. all: 14934 / Num. obs: 14934 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.182 / Χ2: 1.721 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.92-1.985.70.6332.5112150.88299.9
1.98-2.046.60.51512300.945100
2.04-2.117.20.41212400.99100
2.11-2.27.80.36412091.076100
2.2-2.38.30.38312391.609100
2.3-2.429.10.3512431.325100
2.42-2.5710.20.38212562.092100
2.57-2.7710.50.31312332.092100
2.77-3.0510.40.21812431.586100
3.05-3.4910.10.15412481.812100
3.49-4.399.50.13712622.97199.9
4.39-408.90.11713162.17499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N55

3n55


Resolution: 1.92→32.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.376 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 752 5.1 %RANDOM
Rwork0.1682 ---
all0.1696 14872 --
obs0.1696 14872 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.83 Å2 / Biso mean: 29.239 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.92→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 0 118 1012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022946
X-RAY DIFFRACTIONr_bond_other_d0.0030.02601
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9731299
X-RAY DIFFRACTIONr_angle_other_deg0.85131507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19827.17939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47915160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.502151
X-RAY DIFFRACTIONr_chiral_restr0.0990.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02165
X-RAY DIFFRACTIONr_mcbond_it0.9021.5606
X-RAY DIFFRACTIONr_mcbond_other0.2461.5250
X-RAY DIFFRACTIONr_mcangle_it1.5322998
X-RAY DIFFRACTIONr_scbond_it2.2823340
X-RAY DIFFRACTIONr_scangle_it3.6654.5295
LS refinement shellResolution: 1.919→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 64 -
Rwork0.258 1020 -
all-1084 -
obs-1084 99.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76170.0545-0.03841.3409-0.041.13490.0129-0.03940.16130.057-0.00340.273-0.0792-0.0834-0.00950.03580.02920.02660.0752-0.0070.094-18.696810.163854.7058
25.6081-3.5308-2.832227.876-24.425139.025-0.04670.38170.19680.49080.66772.1533-1.17-1.5919-0.6210.20250.1534-0.10370.253-0.00710.6763-27.309917.258445.4852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 116
2X-RAY DIFFRACTION2B117 - 124

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