[English] 日本語
Yorodumi
- PDB-6ld8: Crystal structure of cystathionine gamma synthase from Xanthomona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ld8
TitleCrystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine
ComponentsCystathionine gamma-synthase
KeywordsBIOSYNTHETIC PROTEIN / cysathionine gamma synthase / PLP dependent enzyme / methionine biosynthesis pathway
Function / homology
Function and homology information


carbon-sulfur lyase activity / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
O-succinylhomoserine (thiol)-lyase / 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
Chem-0JO / CYSTEINE / Cystathionine gamma-synthase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNgo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W.
CitationJournal: To Be Published
Title: Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine
Authors: Ngo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystathionine gamma-synthase
B: Cystathionine gamma-synthase
C: Cystathionine gamma-synthase
D: Cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,26112
Polymers172,5114
Non-polymers1,7498
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-98 kcal/mol
Surface area45080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.985, 161.985, 245.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein
Cystathionine gamma-synthase


Mass: 43127.824 Da / Num. of mol.: 4 / Mutation: D134V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85) (bacteria)
Strain: KACC10331 / KXO85 / Gene: metB, XOO1818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H1U9
#2: Chemical
ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.93 Å3/Da / Density % sol: 75.04 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M Ethylene Glycols Mix, 0.1 M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 137559 / % possible obs: 99.94 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.5
Reflection shellResolution: 2.31→2.39 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 13694

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LD7

6ld7


Resolution: 2.31→40.61 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.272 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 6941 5 %RANDOM
Rwork0.1655 ---
obs0.167 131279 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.4 Å2 / Biso mean: 32.296 Å2 / Biso min: 15.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.31→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11491 0 84 597 12172
Biso mean--30.37 36.17 -
Num. residues----1553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01311829
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711162
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.63316106
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5725694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37651549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96521.268568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.047151813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7291584
X-RAY DIFFRACTIONr_chiral_restr0.090.21572
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022491
LS refinement shellResolution: 2.31→2.366 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.251 502 -
Rwork0.235 9681 -
obs--99.61 %

+
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://pdbjlvh1.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