[English] 日本語
Yorodumi
- PDB-3khx: Crystal structure of Staphylococcus aureus metallopeptidase (Sape... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3khx
TitleCrystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the apo-form
ComponentsPutative dipeptidase SACOL1801
KeywordsHYDROLASE / Dipeptidase / DapE / Metallopeptidase / Metal-binding / Metalloprotease / Protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / dipeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M20A, peptidase V-related / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative dipeptidase SACOL1801
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGirish, T.S. / Gopal, B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states
Authors: Girish, T.S. / Gopal, B.
History
DepositionOct 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Nov 1, 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: Putative dipeptidase SACOL1801
B: Putative dipeptidase SACOL1801


Theoretical massNumber of molelcules
Total (without water)110,6792
Polymers110,6792
Non-polymers00
Water3,279182
1
A: Putative dipeptidase SACOL1801


Theoretical massNumber of molelcules
Total (without water)55,3401
Polymers55,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative dipeptidase SACOL1801


Theoretical massNumber of molelcules
Total (without water)55,3401
Polymers55,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.823, 134.172, 68.282
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative dipeptidase SACOL1801 / Metallopeptidase / DapE


Mass: 55339.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: dipeptidase PepV(SACOL1801) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HF23, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: microbatch method under oil / pH: 6.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris, 18.0% PEG 6000, pH 6.5, Microbatch method under oil, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→68.04 Å / Num. obs: 51315 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.085 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7488 / Rsym value: 0.416 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LFW

1lfw


Resolution: 2.3→60.71 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.494 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 2605 5.1 %RANDOM
Rwork0.24557 ---
obs0.24723 48664 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-2.43 Å2
2---3.24 Å20 Å2
3---2.09 Å2
Refine analyzeLuzzati coordinate error free: 0.242 Å
Refinement stepCycle: LAST / Resolution: 2.3→60.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 0 182 6716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226668
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9479048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16625.309324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.707151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4861524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215152
X-RAY DIFFRACTIONr_mcbond_it0.5911.54193
X-RAY DIFFRACTIONr_mcangle_it1.09426699
X-RAY DIFFRACTIONr_scbond_it1.55232475
X-RAY DIFFRACTIONr_scangle_it2.4834.52349
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 179 -
Rwork0.294 3598 -
obs-3598 98.82 %
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)
12.46690.19050.25032.31540.26323.24450.1301-0.1978-0.00790.264-0.1727-0.16640.12780.07430.04260.0578-0.0408-0.00750.11430.01550.01865.9344.01680.3684
21.8933-2.65390.8495.68980.95153.7564-0.2682-0.47260.21360.93380.2602-0.70710.39530.12220.00790.6096-0.1584-0.15380.85730.16030.38939.07114.480116.0846
31.52250.09040.43925.1724-0.96821.75080.00530.02950.13460.22550.02870.1503-0.10960.0157-0.03390.0450.0060.06980.16680.02020.133617.923117.950542.4685
42.0079-1.0427-0.27135.51041.21731.97250.08670.0904-0.0589-0.25-0.0312-0.12640.1452-0.0829-0.05550.04020.0038-0.00340.1230.02320.056113.117656.48369.214
52.5217-0.5351-0.24554.93890.95482.10710.04450.0329-0.15170.2749-0.14210.16270.1099-0.29390.09760.0303-0.0070.0280.09-0.04020.101625.9117-32.99838.9504
65.919-0.79662.27245.26010.47261.14240.1989-0.9867-0.40910.4325-0.41261.52020.2544-0.79520.21370.2452-0.22720.24621.0324-0.35990.81229.7191-33.682838.3811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 178
2X-RAY DIFFRACTION2A390 - 465
3X-RAY DIFFRACTION3B190 - 384
4X-RAY DIFFRACTION4A185 - 384
5X-RAY DIFFRACTION5B6 - 175
6X-RAY DIFFRACTION6B390 - 465

+
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