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- PDB-3njm: P117A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3njm
TitleP117A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.
ComponentsPeptidase
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 / Resolution: 1.64 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 21, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

Deposited unit
A: Peptidase


Theoretical massNumber of molelcules
Total (without water)13,7011
Polymers13,7011
Non-polymers00
Water2,810156
1
A: Peptidase
x 6


Theoretical massNumber of molelcules
Total (without water)82,2036
Polymers82,2036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area13780 Å2
ΔGint-97 kcal/mol
Surface area29080 Å2
MethodPISA
2
A: Peptidase

A: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,4012
Polymers27,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area2390 Å2
ΔGint-17 kcal/mol
Surface area11900 Å2
MethodPISA
3
A: Peptidase

A: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,4012
Polymers27,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.438, 99.438, 101.147
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein Peptidase


Mass: 13700.505 Da / Num. of mol.: 1 / Mutation: P117A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris buffer, 0.3 M magnesium formate, pH 5.5, 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 23, 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: 1.64→28.7 Å / Num. all: 23667 / Num. obs: 23667 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.048 / Χ2: 0.745 / Net I/σ(I): 8.9
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1172 / Χ2: 0.614 / % possible all: 100

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Processing

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

3n55


Resolution: 1.64→28.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.644 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1210 5.2 %RANDOM
Rwork0.163 ---
all0.164 23401 --
obs0.164 23401 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.04 Å2 / Biso mean: 27.996 Å2 / Biso min: 8.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.64→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 0 0 156 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221038
X-RAY DIFFRACTIONr_bond_other_d0.0080.02665
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9791445
X-RAY DIFFRACTIONr_angle_other_deg1.3931682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22427.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49315184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.748152
X-RAY DIFFRACTIONr_chiral_restr0.1820.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
X-RAY DIFFRACTIONr_mcbond_it1.2081.5656
X-RAY DIFFRACTIONr_mcbond_other0.3471.5266
X-RAY DIFFRACTIONr_mcangle_it2.03721096
X-RAY DIFFRACTIONr_scbond_it2.5473382
X-RAY DIFFRACTIONr_scangle_it4.1144.5333
LS refinement shellResolution: 1.641→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 95 -
Rwork0.327 1625 -
all-1720 -
obs-1720 99.48 %
Refinement TLS params.Method: refined / Origin x: 50.2085 Å / Origin y: 7.407 Å / Origin z: 38.0563 Å
111213212223313233
T0.0936 Å20.004 Å20.0046 Å2-0.0195 Å20.0325 Å2--0.0995 Å2
L1.8695 °20.1053 °20.0441 °2-1.0784 °20.0559 °2--1.3288 °2
S0.0058 Å °-0.081 Å °-0.3707 Å °0.0473 Å °-0.0131 Å °0.0206 Å °0.1494 Å °-0.0586 Å °0.0074 Å °

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