[English] 日本語
Yorodumi
- PDB-9j7p: Crystal structure of S. aureus MccB mutant S323A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j7p
TitleCrystal structure of S. aureus MccB mutant S323A
ComponentsCystathionine gamma-synthase homolog
KeywordsLYASE / CGL / PLP / MccB
Function / homology
Function and homology information


cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Cystathionine gamma-synthase homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHa, N.-C. / Lee, D. / Lee, H. / Byun, K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2021-IP321036 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A2C109178313 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of S. aureus MccB mutant S323A
Authors: Ha, N.-C. / Lee, D. / Lee, H. / Byun, K.
History
DepositionAug 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystathionine gamma-synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4632
Polymers41,3671
Non-polymers961
Water46826
1
A: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
hetero molecules

A: Cystathionine gamma-synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,8518
Polymers165,4674
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area17150 Å2
ΔGint-159 kcal/mol
Surface area47500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.175, 105.175, 289.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

-
Components

#1: Protein Cystathionine gamma-synthase homolog


Mass: 41366.762 Da / Num. of mol.: 1 / Mutation: S323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: yrhB, SAV0460 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JQ19
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.78 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 2% PEG400, 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 42307 / % possible obs: 99.8 % / Redundancy: 15.9 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Rrim(I) all: 0.082 / Net I/σ(I): 30.36
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 5.25 / Num. unique obs: 2070 / CC1/2: 0.951 / Rpim(I) all: 0.087 / Rrim(I) all: 0.283 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→33.26 Å / SU ML: 0.2417 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 19.9123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 2000 4.9 %
Rwork0.1932 38789 -
obs0.1946 40789 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.89 Å2
Refinement stepCycle: LAST / Resolution: 2.19→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 5 26 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592835
X-RAY DIFFRACTIONf_angle_d0.8183857
X-RAY DIFFRACTIONf_chiral_restr0.0536471
X-RAY DIFFRACTIONf_plane_restr0.007489
X-RAY DIFFRACTIONf_dihedral_angle_d5.6966391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.27591030.23951992X-RAY DIFFRACTION70.8
2.24-2.30.28311260.24062454X-RAY DIFFRACTION87.07
2.3-2.370.27911390.23622681X-RAY DIFFRACTION93.97
2.37-2.450.26061430.23512773X-RAY DIFFRACTION97.66
2.45-2.530.24571440.23162798X-RAY DIFFRACTION99.32
2.54-2.640.26871450.21492837X-RAY DIFFRACTION99.67
2.64-2.760.24551480.20812861X-RAY DIFFRACTION99.83
2.76-2.90.21361480.21042850X-RAY DIFFRACTION99.83
2.9-3.080.22271460.19672847X-RAY DIFFRACTION99.87
3.08-3.320.21511480.19962875X-RAY DIFFRACTION99.9
3.32-3.650.21461490.19492875X-RAY DIFFRACTION99.9
3.66-4.180.21511500.16752913X-RAY DIFFRACTION99.9
4.18-5.270.17821520.15362946X-RAY DIFFRACTION100
5.27-33.260.20731590.17183087X-RAY DIFFRACTION99.91

+
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