[English] 日本語
Yorodumi
- PDB-7rzb: BrxA from Staphylococcus aureus with bacillithiol mixed disulfide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rzb
TitleBrxA from Staphylococcus aureus with bacillithiol mixed disulfide
ComponentsBacillithiol system oxidoreductase, YphP/YqiW family
KeywordsOXIDOREDUCTASE / Bacillithiol / redox / oxidative stress / bacilliredoxin
Function / homologyBacilliredoxins BrxB/BrxA / Disulphide isomerase / Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / Chem-G5M / PHOSPHATE ION / Bacillithiol system oxidoreductase, YphP/YqiW family
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCook, P.D. / McHugh, C.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM117488 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structure of BrxA from Staphylococcus aureus, a bacilliredoxin involved in redox homeostasis in Firmicutes.
Authors: McHugh, C.S. / Cook, P.D.
History
DepositionAug 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacillithiol system oxidoreductase, YphP/YqiW family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7713
Polymers16,2781
Non-polymers4932
Water2,234124
1
A: Bacillithiol system oxidoreductase, YphP/YqiW family
hetero molecules

A: Bacillithiol system oxidoreductase, YphP/YqiW family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5436
Polymers32,5562
Non-polymers9874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2080 Å2
ΔGint-29 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.882, 84.882, 41.037
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-202-

PO4

21A-388-

HOH

31A-389-

HOH

41A-413-

HOH

-
Components

#1: Protein Bacillithiol system oxidoreductase, YphP/YqiW family / BrxA/BrxB family bacilliredoxin


Mass: 16278.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: A2U18_07020, C7P97_04720, CSC83_09870, CSC87_03980, GF559_09020, HU771_05980, SAMEA70245418_01058
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A229LVN5
#2: Chemical ChemComp-G5M / (2S)-2-{[2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid


Mass: 398.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N2O10S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM ammonium phosphate, 10% w/v PEG3350, 10 mM HEPES, 25 mM sodium chloride, 18 mg/mL BrxA, 1 mM bacillithiol disulfide
PH range: 5.0-6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→60.02 Å / Num. all: 20331 / Num. obs: 20331 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.75 Å2 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Rsym value: 0.043 / Net I/av σ(I): 10.2 / Net I/σ(I): 16.1 / Num. measured all: 131867
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.694.20.5891.31198028560.3140.6720.5891.798.5
1.69-1.795.60.3042.51557727710.140.3350.3043.699.9
1.79-1.916.90.1933.71796925890.0790.2090.1936.3100
1.91-2.077.30.11261771124400.0450.120.11210.9100
2.07-2.267.30.0758.21647122570.0310.0810.07516100
2.26-2.537.20.0688.51481020450.0280.0740.06820.4100
2.53-2.927.20.069.81318418330.0250.0650.0626.8100
2.92-3.587.10.03816.31104215550.0150.0410.03837.5100
3.58-5.066.90.02722.4858212430.0110.0290.02743.999.9
5.06-33.8766.10.02324.545417420.010.0260.02339.999.4

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FHK

3fhk


Resolution: 1.6→33.876 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1044 5.16 %
Rwork0.1961 19190 -
obs0.1975 20234 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.13 Å2 / Biso mean: 36.1551 Å2 / Biso min: 20.76 Å2
Refinement stepCycle: final / Resolution: 1.6→33.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 31 124 1201
Biso mean--38.93 43.9 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061118
X-RAY DIFFRACTIONf_angle_d0.8611524
X-RAY DIFFRACTIONf_chiral_restr0.056175
X-RAY DIFFRACTIONf_plane_restr0.004207
X-RAY DIFFRACTIONf_dihedral_angle_d6.82908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.6840.33191320.2776262497
1.684-1.78950.30131390.2322271399
1.7895-1.92770.2871610.21952684100
1.9277-2.12160.26681550.20252708100
2.1216-2.42860.24341640.20262745100
2.4286-3.05940.21431450.20672771100
3.0594-33.8760.19211480.17792945100

+
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