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- PDB-3njj: P115A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3njj
TitleP115A 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 / Resolution: 1.56 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 1.3Oct 31, 2012Group: Derived calculations
Revision 1.4Nov 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 1.5Sep 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)13,7192
Polymers13,7192
Non-polymers00
Water2,576143
1
A: Peptidase
B: Peptidase
x 6


Theoretical massNumber of molelcules
Total (without water)82,31112
Polymers82,31112
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 area19670 Å2
ΔGint-124 kcal/mol
Surface area27920 Å2
MethodPISA
2
A: Peptidase
B: Peptidase

A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,4374
Polymers27,4374
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5020 Å2
ΔGint-29 kcal/mol
Surface area10850 Å2
MethodPISA
3
A: Peptidase
B: Peptidase

A: Peptidase
B: Peptidase


Theoretical massNumber of molelcules
Total (without water)27,4374
Polymers27,4374
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area3820 Å2
ΔGint-21 kcal/mol
Surface area12040 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.104, 100.104, 101.086
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: 12638.304 Da / Num. of mol.: 1 / Fragment: N-terminal domain 1-116 / Mutation: P115A
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.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.55 Å3/Da / Density % sol: 65.38 %
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 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: 1.56→28.9 Å / Num. all: 27489 / Num. obs: 27489 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.046 / Χ2: 0.977 / Net I/σ(I): 10.8
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1448 / Χ2: 0.826 / % possible all: 90.6

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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: 1.56→28.9 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.222 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.181 2083 7.7 %RANDOM
Rwork0.154 ---
all0.157 27165 --
obs0.157 27165 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.75 Å2 / Biso mean: 13.53 Å2 / Biso min: 2.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.56→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 0 143 1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022969
X-RAY DIFFRACTIONr_bond_other_d0.0030.02621
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9721336
X-RAY DIFFRACTIONr_angle_other_deg0.94531565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.89727.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02215172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg42.484151
X-RAY DIFFRACTIONr_chiral_restr0.1160.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02170
X-RAY DIFFRACTIONr_mcbond_it1.7951.5615
X-RAY DIFFRACTIONr_mcbond_other0.5831.5254
X-RAY DIFFRACTIONr_mcangle_it2.70821019
X-RAY DIFFRACTIONr_scbond_it3.8333354
X-RAY DIFFRACTIONr_scangle_it5.774.5306
X-RAY DIFFRACTIONr_rigid_bond_restr1.61831590
LS refinement shellResolution: 1.562→1.602 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 148 -
Rwork0.284 1692 -
all-1840 -
obs-1840 91.72 %
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)
10.8838-0.1790.00540.2743-0.06540.7595-0.02110.04810.186-0.0290.0079-0.012-0.1025-0.01060.01310.2252-0.0056-0.00370.13620.02460.19760.805721.204646.1001
224.5154-9.0481-21.137510.355812.057734.3029-0.06960.95342.6924-0.7145-0.4627-0.1334-2.85860.03570.53240.6957-0.0282-0.38320.05030.14130.8898-1.307232.306355.127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 116
2X-RAY DIFFRACTION2B117 - 124

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