[English] 日本語
Yorodumi
- PDB-6le4: Crystal structure of cystathionine gamma-lyase from Lactobacillus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6le4
TitleCrystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with cystathionine
ComponentsCystathionine gamma-lyase
KeywordsLYASE / cystathionine gamma-lyase
Function / homology
Function and homology information


: / cystathionine gamma-synthase activity / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / transaminase activity / pyridoxal phosphate binding / lyase activity
Similarity search - Function
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-E9U / PHOSPHATE ION / Aminotransferase class V-fold PLP-dependent enzyme / Cystathionine beta-lyase / cystathionine gamma-lyase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOda, K. / Matoba, Y.
CitationJournal: Sci Rep / Year: 2020
Title: Catalytic specificity of the Lactobacillus plantarum cystathionine gamma-lyase presumed by the crystallographic analysis.
Authors: Matoba, Y. / Noda, M. / Yoshida, T. / Oda, K. / Ezumi, Y. / Yasutake, C. / Izuhara-Kihara, H. / Danshiitsoodol, N. / Kumagai, T. / Sugiyama, M.
History
DepositionNov 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 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-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,48715
Polymers251,4936
Non-polymers2,9939
Water5,332296
1
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,75311
Polymers167,6624
Non-polymers2,0907
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-113 kcal/mol
Surface area43310 Å2
MethodPISA
2
E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
hetero molecules

E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,4688
Polymers167,6624
Non-polymers1,8064
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area18720 Å2
ΔGint-98 kcal/mol
Surface area43480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.568, 200.738, 114.883
Angle α, β, γ (deg.)90.000, 117.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-1249-

HOH

21E-1255-

HOH

31F-1286-

HOH

-
Components

#1: Protein
Cystathionine gamma-lyase / Cystathionine gamma-synthase


Mass: 41915.562 Da / Num. of mol.: 6 / Fragment: Cystathionine gamma-lyase / Mutation: K194A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: BIZ32_00995, Nizo2891_3187 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A162EFJ4, UniProt: F9UT53*PLUS
#2: Chemical
ChemComp-E9U / (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid


Mass: 451.389 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N3O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 4.42 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: KH2PO4, NaH2PO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2014 / Details: mirros
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.083→100 Å / Num. obs: 72733 / % possible obs: 91.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.123 / Rrim(I) all: 0.189 / Χ2: 1.01 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.2120.43474690.7610.3740.5750.7894.2
3.21-3.3420.34173870.8170.2940.4520.85493.6
3.34-3.4920.25774210.8940.2210.340.9493.5
3.49-3.6820.21174000.9150.1810.2790.93493.1
3.68-3.9120.17173080.9410.1470.2271.04592.4
3.91-4.2120.13573030.9590.1160.1791.06191.8
4.21-4.6320.11172430.970.0960.1471.1991
4.63-5.32.10.09871770.9780.0840.131.11390.1
5.3-6.6820.10870900.9720.0930.1430.9888.8
6.68-1002.20.06169350.990.0520.0811.18386.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4L0O

4l0o


Resolution: 3.1→36.257 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2725 3656 5.03 %
Rwork0.2457 --
obs0.2471 72703 90.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 341.95 Å2 / Biso mean: 39.3219 Å2 / Biso min: 0.77 Å2
Refinement stepCycle: final / Resolution: 3.1→36.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17208 0 189 297 17694
Biso mean--38.43 19.31 -
Num. residues----2280
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.12370.36461170.3085208672
3.1237-3.16650.31031270.2997277594
3.1665-3.21170.31291570.295275294
3.2117-3.25960.32341380.2946272094
3.2596-3.31050.32751360.2819273494
3.3105-3.36480.33281490.2696274894
3.3648-3.42270.24751400.2573273093
3.4227-3.48490.27171530.2537272093
3.4849-3.55190.3041400.2522269993
3.5519-3.62430.28821520.2568271593
3.6243-3.70310.27391050.2427276193
3.7031-3.78910.24241210.2437274192
3.7891-3.88380.26791580.2405267392
3.8838-3.98860.26551220.2253272192
3.9886-4.10590.24251470.2272268491
4.1059-4.23820.26381430.2302266592
4.2382-4.38940.2391650.2247265991
4.3894-4.56480.26431420.2079263591
4.5648-4.77220.22631590.215263590
4.7722-5.02320.23141450.2145263390
5.0232-5.33690.23821330.2243263390
5.3369-5.74750.26061460.2202264289
5.7475-6.32320.27051400.2418260389
6.3232-7.23180.26811440.2573257588
7.2318-9.08760.26851260.233259987
9.0876-36.2570.31211510.287250984

+
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