[English] 日本語
Yorodumi
- PDB-6jis: Crystal structure of the histidine racemase CntK in cobalt and ni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jis
TitleCrystal structure of the histidine racemase CntK in cobalt and nickel transporter system of staphylococcus aureus
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / histidine racemase / cobalt and nickel transporter system
Function / homologyhistidine racemase / isomerase activity / cytoplasm / : / Histidine racemase / Diaminopimelate epimerase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLuo, S. / Ju, Y. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
National Science Foundation (China)81803435 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure of CntK, the cofactor-independent histidine racemase in staphylopine-mediated metal acquisition of Staphylococcus aureus.
Authors: Luo, S. / Ju, Y. / Zhou, J. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionFeb 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,88415
Polymers32,5991
Non-polymers1,28514
Water3,495194
1
A: Diaminopimelate epimerase
hetero molecules

A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,76730
Polymers65,1972
Non-polymers2,57028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6350 Å2
ΔGint-474 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.850, 60.374, 76.755
Angle α, β, γ (deg.)90.00, 116.09, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Diaminopimelate epimerase / Histidine racemase CntK


Mass: 32598.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cntK, dapF, D5R87_08325, D5R88_09755, M1K003_1013 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A389TBD7, UniProt: A0A0H3JU78*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.47 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% pEG 3350.

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.82→32.24 Å / Num. obs: 25303 / % possible obs: 96.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 1.82→1.86 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1523

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIW

6jiw


Resolution: 1.82→32.24 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.275 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.143 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24861 1245 4.9 %RANDOM
Rwork0.19545 ---
obs0.19797 24057 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.533 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å2-0 Å20.84 Å2
2---1.65 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.82→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 26 194 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171841
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6362867
X-RAY DIFFRACTIONr_angle_other_deg1.3531.564271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71423.83899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97515330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.704156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7262.2061060
X-RAY DIFFRACTIONr_mcbond_other1.7262.2051059
X-RAY DIFFRACTIONr_mcangle_it2.6973.3011325
X-RAY DIFFRACTIONr_mcangle_other2.6963.3011326
X-RAY DIFFRACTIONr_scbond_it2.2712.4841053
X-RAY DIFFRACTIONr_scbond_other2.272.4841054
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.553.6111543
X-RAY DIFFRACTIONr_long_range_B_refined5.73627.8612360
X-RAY DIFFRACTIONr_long_range_B_other5.59327.5382321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 104 -
Rwork0.259 1821 -
obs--97.37 %

+
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