[English] 日本語
Yorodumi
- PDB-3nji: S114A mutant of SO1698 protein, an aspartic peptidase from Shewan... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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.

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more