[English] 日本語
Yorodumi
- PDB-4xch: S-ribosylhomocysteinase from Streptococcus suis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xch
TitleS-ribosylhomocysteinase from Streptococcus suis
ComponentsS-ribosylhomocysteine lyase
KeywordsLYASE / S-ribosylhomocysteinase
Function / homology
Function and homology information


S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / quorum sensing / iron ion binding
Similarity search - Function
S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) superfamily / S-Ribosylhomocysteinase (LuxS) / Metalloenzyme, LuxS/M16 peptidase-like / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWang, Y. / Mao, X. / Lu, C.
CitationJournal: To Be Published
Title: Crystal Structure of LuxS from Streptococcus suis
Authors: Wang, Y. / Mao, X. / Lu, C.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-ribosylhomocysteine lyase
B: S-ribosylhomocysteine lyase
C: S-ribosylhomocysteine lyase
D: S-ribosylhomocysteine lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5328
Polymers86,2704
Non-polymers2624
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-184 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.890, 86.250, 103.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
S-ribosylhomocysteine lyase / S-ribosylhomocysteinase / AI-2 synthesis protein / Autoinducer-2 production protein LuxS


Mass: 21567.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: HA9801 / Gene: luxS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: B2CMA5, S-ribosylhomocysteine lyase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M potassium-sodium tartrate, 0.1M sodium citrate (pH 6.5), 1M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→38.2 Å / Num. obs: 50447 / % possible obs: 99.03 % / Redundancy: 13.8 % / Net I/σ(I): 6.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.2→38.177 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1713 5.14 %
Rwork0.1849 --
obs0.1874 33347 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 4 137 4825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084776
X-RAY DIFFRACTIONf_angle_d1.1466459
X-RAY DIFFRACTIONf_dihedral_angle_d13.7221785
X-RAY DIFFRACTIONf_chiral_restr0.077732
X-RAY DIFFRACTIONf_plane_restr0.004827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.26480.31761330.23652360X-RAY DIFFRACTION88
2.2648-2.33790.27871310.22482460X-RAY DIFFRACTION91
2.3379-2.42140.25351350.20572496X-RAY DIFFRACTION93
2.4214-2.51830.2711380.19962553X-RAY DIFFRACTION94
2.5183-2.63290.30431310.2052567X-RAY DIFFRACTION95
2.6329-2.77170.24741440.20442638X-RAY DIFFRACTION96
2.7717-2.94530.24581520.19552648X-RAY DIFFRACTION98
2.9453-3.17260.22711400.19652709X-RAY DIFFRACTION98
3.1726-3.49170.21451550.1832727X-RAY DIFFRACTION100
3.4917-3.99650.23091340.1642778X-RAY DIFFRACTION100
3.9965-5.03330.18831570.15252789X-RAY DIFFRACTION100
5.0333-38.18230.21741630.1812909X-RAY DIFFRACTION100

+
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