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- PDB-3nji: S114A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3nji
TitleS114A 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: 1.8 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 1.0Sep 22, 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)14,7912
Polymers14,7912
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-6 kcal/mol
Surface area6800 Å2
Unit cell
Length a, b, c (Å)99.833, 99.833, 99.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Peptidase


Mass: 13710.542 Da / Num. of mol.: 1 / Mutation: S114A
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.: 104 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE AUTHORS STATE THAT THERE IS A PARTIAL HYDROLYSIS OF THE BOND BETWEEN RESIDUES 116 AND 117. FOR ...THE AUTHORS STATE THAT THERE IS A PARTIAL HYDROLYSIS OF THE BOND BETWEEN RESIDUES 116 AND 117. FOR RESIDUES 115-123, CONFORMER A REPRESENTS UNCLEAVED PROTEIN WITH A BOND BETWEEN RESIDUES 116-117. CONFORMER B REPRESENTS CLEAVED CHAIN AND THERE IS NO COVALENT BOND BETWEEN RESIDUES A116 AND B117 DUE TO 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M ammonium sulfate, 0.1 M Bis-Tris buffer, 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-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008
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: 1.8→43.2 Å / Num. all: 17886 / Num. obs: 17886 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.432 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.834.80.6131.978240.80694.2
1.83-1.865.90.5598640.83297.7
1.86-1.97.40.5568970.919100
1.9-1.949.50.4158770.973100
1.94-1.9810.40.3688891.049100
1.98-2.0310.60.3038971.108100
2.03-2.0810.80.2469011.204100
2.08-2.1310.70.2078901.373100
2.13-2.210.70.1918741.516100
2.2-2.2710.80.1688991.593100
2.27-2.3510.70.1578941.75100
2.35-2.4410.60.1388981.788100
2.44-2.5510.60.1198891.866100
2.55-2.6910.60.1078981.738100
2.69-2.8610.50.0919071.67100
2.86-3.0810.20.0758941.585100
3.08-3.39100.0649101.463100
3.39-3.889.70.0599061.435100
3.88-4.889.70.0549231.5699.9
4.88-50100.0459551.48399.4

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Processing

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

3n55


Resolution: 1.8→43.2 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.535 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 907 5.1 %RANDOM
Rwork0.1663 ---
all0.1674 17729 --
obs0.1674 17729 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.69 Å2 / Biso mean: 41.472 Å2 / Biso min: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å20 Å2
2--0.43 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 0 104 1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221044
X-RAY DIFFRACTIONr_bond_other_d0.0020.02681
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9821438
X-RAY DIFFRACTIONr_angle_other_deg0.89231710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.42327.04544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49115181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.525152
X-RAY DIFFRACTIONr_chiral_restr0.1090.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
X-RAY DIFFRACTIONr_mcbond_it1.011.5663
X-RAY DIFFRACTIONr_mcbond_other0.2941.5268
X-RAY DIFFRACTIONr_mcangle_it1.721099
X-RAY DIFFRACTIONr_scbond_it2.3743381
X-RAY DIFFRACTIONr_scangle_it3.8314.5330
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 62 -
Rwork0.313 1065 -
all-1127 -
obs-1127 85.31 %
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)
10.8567-0.18030.21361.16670.06191.45450.00240.00090.13710.0044-0.03540.2007-0.0962-0.120.0330.02030.02230.01040.0571-0.01080.0789-18.685710.170954.2317
25.7783-1.7237-3.776414.1024-3.168115.077-0.0806-0.02840.42320.72710.22540.968-0.5899-1.2488-0.14480.22640.0927-0.06190.278-0.00360.2835-27.622917.169344.8112
323.8354-25.208322.332148.4833-8.090831.97310.89882.492-0.7999-1.9863-3.27965.0559-0.16461.75462.38080.57880.5512-0.10030.7092-0.23221.2834-27.412117.42844.9583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 116
2X-RAY DIFFRACTION2A117 - 124
3X-RAY DIFFRACTION3B117 - 124

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