[English] 日本語
Yorodumi
- PDB-6gmz: Staphylopine dehydrogenase in complex with Histidine tag and citrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gmz
TitleStaphylopine dehydrogenase in complex with Histidine tag and citrate
Components
  • ALA-HIS-HIS-ALA
  • Staphylopine dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / staphylopine biosynthesis
Function / homologystaphylopine dehydrogenase / : / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / CITRIC ACID / AMMONIUM ION / Staphylopine synthase / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsHajjar, C. / Arnoux, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0007-02 France
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis.
Authors: Hajjar, C. / Fanelli, R. / Laffont, C. / Brutesco, C. / Cullia, G. / Tribout, M. / Nurizzo, D. / Borezee-Durant, E. / Voulhoux, R. / Pignol, D. / Lavergne, J. / Cavelier, F. / Arnoux, P.
History
DepositionMay 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Staphylopine dehydrogenase
B: ALA-HIS-HIS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4565
Polymers55,0522
Non-polymers4043
Water3,891216
1
A: Staphylopine dehydrogenase
B: ALA-HIS-HIS-ALA
hetero molecules

A: Staphylopine dehydrogenase
B: ALA-HIS-HIS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,91210
Polymers110,1044
Non-polymers8096
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6940 Å2
ΔGint-13 kcal/mol
Surface area37190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.440, 48.790, 60.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Staphylopine dehydrogenase


Mass: 54615.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: APW47_05390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q4GXD5, UniProt: A0A0H3JT80*PLUS
#2: Protein/peptide ALA-HIS-HIS-ALA


Mass: 436.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 219 molecules

#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium citrate tribasic dihydrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52360 / % possible obs: 98.6 % / Redundancy: 6.7 % / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.3 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2.22→47.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.821 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24889 1438 5.1 %RANDOM
Rwork0.18061 ---
obs0.18403 26559 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.22→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 27 216 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193606
X-RAY DIFFRACTIONr_bond_other_d0.0020.023339
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9864867
X-RAY DIFFRACTIONr_angle_other_deg1.02937790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93624.941170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32415603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4871514
X-RAY DIFFRACTIONr_chiral_restr0.1080.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213914
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02696
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_it3.8094.5741726
X-RAY DIFFRACTIONr_mcbond_other3.7944.5721725
X-RAY DIFFRACTIONr_mcangle_it5.1786.8442154
X-RAY DIFFRACTIONr_mcangle_other5.1776.8462155
X-RAY DIFFRACTIONr_scbond_it5.3465.2011880
X-RAY DIFFRACTIONr_scbond_other5.3455.2021881
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8777.5342714
X-RAY DIFFRACTIONr_long_range_B_refined9.20854.4793972
X-RAY DIFFRACTIONr_long_range_B_other9.19654.3433939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.215→2.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 103 -
Rwork0.339 1763 -
obs--92.7 %

+
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