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- PDB-3njk: D116A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3njk
TitleD116A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis, at pH5.5
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: 1.5 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7752
Polymers13,6831
Non-polymers921
Water2,774154
1
A: Peptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)82,64812
Polymers82,0956
Non-polymers5536
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 area15590 Å2
ΔGint-101 kcal/mol
Surface area28350 Å2
MethodPISA
2
A: Peptidase
hetero molecules

A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5494
Polymers27,3652
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2750 Å2
ΔGint-18 kcal/mol
Surface area11890 Å2
MethodPISA
3
A: Peptidase
hetero molecules

A: Peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5494
Polymers27,3652
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area2350 Å2
ΔGint-14 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.013, 99.013, 101.037
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: 13682.532 Da / Num. of mol.: 1 / Mutation: D116A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M ammonium sulfate, 0.1 M Bis-Tris, 1% PEG-3350, 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: 1.5→28.6 Å / Num. all: 30415 / Num. obs: 30415 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.042 / Χ2: 0.967 / Net I/σ(I): 11.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.08 / Num. unique all: 1444 / Χ2: 1.041 / % possible all: 95.4

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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: 1.5→28.58 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.77 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1550 5.1 %RANDOM
Rwork0.154 ---
all0.155 30386 --
obs0.155 30386 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.08 Å2 / Biso mean: 24.873 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 6 154 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221032
X-RAY DIFFRACTIONr_bond_other_d0.0020.02662
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9841433
X-RAY DIFFRACTIONr_angle_other_deg1.02131673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.40826.90542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48815178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.688152
X-RAY DIFFRACTIONr_chiral_restr0.1150.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02181
X-RAY DIFFRACTIONr_mcbond_it1.1461.5654
X-RAY DIFFRACTIONr_mcbond_other0.3271.5264
X-RAY DIFFRACTIONr_mcangle_it1.94621092
X-RAY DIFFRACTIONr_scbond_it2.5773378
X-RAY DIFFRACTIONr_scangle_it4.0774.5327
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 125 -
Rwork0.313 2017 -
all-2142 -
obs-2142 95.16 %
Refinement TLS params.Method: refined / Origin x: 19.1488 Å / Origin y: 11.2534 Å / Origin z: 54.1984 Å
111213212223313233
T0.0361 Å2-0.0325 Å2-0.0223 Å2-0.0631 Å2-0.0063 Å2--0.0981 Å2
L1.2065 °2-0.4688 °20.0492 °2-1.3391 °20.0767 °2--0.7971 °2
S-0.027 Å °-0.0315 Å °0.2044 Å °0.0423 Å °0.0232 Å °-0.331 Å °-0.0357 Å °0.132 Å °0.0038 Å °

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