[English] 日本語
Yorodumi
- PDB-7ysl: Crystal structure of D-Cysteine desulfhydrase with a trapped PLP-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ysl
TitleCrystal structure of D-Cysteine desulfhydrase with a trapped PLP-pyruvate geminal diamine
ComponentsD-Cysteine desulfhydrase
KeywordsLYASE / PLP-dependent enzyme / D-Cysteine desulfhydrase / geminal diamine
Function / homology
Function and homology information


L-cysteate sulfo-lyase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity
Similarity search - Function
D-cysteine desulfhydrase / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
FORMIC ACID / L-cysteate sulfo-lyase
Similarity search - Component
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsZhang, X. / Wang, L. / Xu, X. / Xing, X. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA09005000 China
CitationJournal: Tetrahedron / Year: 2022
Title: Characterization and structural basis of D-cysteine desulfhydrase from Pectobacterium atrosepticum
Authors: Xu, X. / Yang, L. / Zhang, X. / Xing, X. / Zhou, J.
History
DepositionAug 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 2.0Feb 8, 2023Group: Atomic model / Derived calculations / Category: atom_site / struct_conf
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Revision 3.0Nov 29, 2023Group: Data collection / Polymer sequence ...Data collection / Polymer sequence / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity_poly / pdbx_initial_refinement_model
Item: _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code_can

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-Cysteine desulfhydrase
B: D-Cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,84317
Polymers80,1042
Non-polymers73915
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-7 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.380, 85.478, 123.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein D-Cysteine desulfhydrase


Mass: 40052.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA1531 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D6Z8, D-cysteine desulfhydrase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Carboxylic acids (sodium formate, ammonium acetate, sodium citrate, potassium sodium tartrate, sodium oxamate), 0.1 M imidazole/MES pH 6.5, 30% (v/v) PEG 500 MME/PEG 20000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.02→123.09 Å / Num. obs: 46857 / % possible obs: 97.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3518 / CC1/2: 0.746 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D97

4d97


Resolution: 2.02→70.21 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 2180 4.66 %
Rwork0.1718 44583 -
obs0.1735 46763 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101 Å2 / Biso mean: 31.1538 Å2 / Biso min: 15.19 Å2
Refinement stepCycle: final / Resolution: 2.02→70.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 48 311 5511
Biso mean--48.15 36.4 -
Num. residues----676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.060.27911380.230128262964100
2.06-2.110.28091420.226628042946100
2.11-2.160.27981330.201828142947100
2.16-2.220.20911460.186228102956100
2.22-2.290.27981230.19752225234879
2.29-2.360.21741230.176228532976100
2.36-2.450.22181400.178328182958100
2.45-2.550.25431160.181328592975100
2.55-2.660.21271210.178928552976100
2.66-2.80.2321400.178828432983100
2.8-2.980.19591420.167428542996100
2.98-3.210.24621420.171428552997100
3.21-3.530.17611460.164628813027100
3.53-4.040.17211210.15492338245981
4.04-5.090.18321540.140728953049100
5.09-70.210.19521530.18143053320699

+
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