[English] 日本語
Yorodumi
- PDB-8wkr: Crystal structure of O-acetylhomoserine sulfhydrylase from Lactob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wkr
TitleCrystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the open form
ComponentsL-methionine gamma-lyase
KeywordsLYASE / O-acetylhomoserine sulfhydrylase
Function / homology
Function and homology information


O-acetylhomoserine aminocarboxypropyltransferase / O-acetylhomoserine aminocarboxypropyltransferase activity / cystathionine gamma-synthase / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding
Similarity search - Function
O-acetylhomoserine/O-acetylserine sulfhydrylase / 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-LLP / PROLINE / L-methionine gamma-lyase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum JDM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Environ.Microbiol. / Year: 2024
Title: pH-dependent regulation of an acidophilic O -acetylhomoserine sulfhydrylase from Lactobacillus plantarum.
Authors: Matoba, Y. / Oda, K. / Wataeda, M. / Kanemori, H. / Matsuo, K.
History
DepositionSep 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-methionine gamma-lyase
B: L-methionine gamma-lyase
C: L-methionine gamma-lyase
D: L-methionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,77810
Polymers192,0464
Non-polymers1,7326
Water19,7441096
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18480 Å2
ΔGint-97 kcal/mol
Surface area50940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.281, 114.929, 98.911
Angle α, β, γ (deg.)90.00, 110.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
L-methionine gamma-lyase


Mass: 48011.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum JDM1 (bacteria)
Gene: mgl / Plasmid: pET28 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: A0A0G9F7S9
#2: Chemical
ChemComp-LLP / (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid / N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE


Type: L-peptide linking / Mass: 375.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N3O7P
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1096 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 4000, Li2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. obs: 110187 / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.105 / Χ2: 1.033 / Net I/σ(I): 6.1 / Num. measured all: 390903
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.05-2.123.60.412110000.5221100
2.12-2.213.60.333109390.578199.9
2.21-2.313.60.273109870.658199.9
2.31-2.433.60.234110080.7231100
2.43-2.583.60.193110000.793199.9
2.58-2.783.60.151110280.957199.9
2.78-3.063.60.119109651.147199.9
3.06-3.513.50.092110801.416199.9
3.51-4.423.50.068110511.883199.8
4.42-1003.30.054111291.785199.3

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→39.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 5702 5.18 %
Rwork0.1526 --
obs0.1548 110113 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12348 0 16 1096 13460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712716
X-RAY DIFFRACTIONf_angle_d0.81717384
X-RAY DIFFRACTIONf_dihedral_angle_d16.51767
X-RAY DIFFRACTIONf_chiral_restr0.0532035
X-RAY DIFFRACTIONf_plane_restr0.0052259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.23841730.17833113X-RAY DIFFRACTION90
2.07-2.10.25751890.18463493X-RAY DIFFRACTION100
2.1-2.120.22451960.18473469X-RAY DIFFRACTION100
2.12-2.150.24292010.17433495X-RAY DIFFRACTION100
2.15-2.180.18561610.17333467X-RAY DIFFRACTION100
2.18-2.210.25921670.16823509X-RAY DIFFRACTION100
2.21-2.240.19742060.15843481X-RAY DIFFRACTION100
2.24-2.270.19241950.15873466X-RAY DIFFRACTION100
2.27-2.310.22441870.15323485X-RAY DIFFRACTION100
2.31-2.350.20811750.15643518X-RAY DIFFRACTION100
2.35-2.390.21632000.15183455X-RAY DIFFRACTION100
2.39-2.430.21670.15273527X-RAY DIFFRACTION100
2.43-2.480.21452050.15513492X-RAY DIFFRACTION100
2.48-2.530.23082090.16583452X-RAY DIFFRACTION100
2.53-2.580.19181830.15523505X-RAY DIFFRACTION100
2.58-2.640.22481980.15553489X-RAY DIFFRACTION100
2.64-2.710.19721960.15763454X-RAY DIFFRACTION100
2.71-2.780.20512130.15783475X-RAY DIFFRACTION100
2.78-2.860.20551980.15673497X-RAY DIFFRACTION100
2.86-2.960.21652170.15443459X-RAY DIFFRACTION100
2.96-3.060.20881680.15473504X-RAY DIFFRACTION100
3.06-3.180.19281810.1543514X-RAY DIFFRACTION100
3.18-3.330.20261980.15183484X-RAY DIFFRACTION100
3.33-3.50.18651870.153514X-RAY DIFFRACTION100
3.5-3.720.19241730.14623502X-RAY DIFFRACTION100
3.72-4.010.17512120.1333500X-RAY DIFFRACTION100
4.01-4.410.14451850.12623516X-RAY DIFFRACTION100
4.41-5.050.17561970.13333502X-RAY DIFFRACTION100
5.05-6.360.18821700.16673551X-RAY DIFFRACTION100
6.36-39.530.17111950.163523X-RAY DIFFRACTION98

+
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