4XCH | pdb_00004xch

S-ribosylhomocysteinase from Streptococcus suis

PDB DOI: https://doi.org/10.2210/pdb4XCH/pdb

Classification: LYASE
Organism(s): Streptococcus suis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-12-18 Released: 2015-06-24
Deposition Author(s): Wang, Y., Mao, X., Lu, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of LuxS from Streptococcus suis

Wang, Y., Mao, X., Lu, C.

To be published.

Macromolecule Content

Total Structure Weight: 86.53 kDa
Atom Count: 4,825
Modeled Residue Count: 596
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-ribosylhomocysteine lyase	A, B, C, D	194	Streptococcus suis	Mutation(s): 0 Gene Names: luxS EC: 4.4.1.21
UniProt
Find proteins for B2CMA5 (Streptococcus suis) Explore B2CMA5 Go to UniProtKB: B2CMA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2CMA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.89	α = 90
b = 86.25	β = 90
c = 103.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data processing
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Wang, Y.

Mao, X.

Lu, C.

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2017-10-04
Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

4XCH | pdb_00004xch

S-ribosylhomocysteinase from Streptococcus suis

Literature

Crystal Structure of LuxS from Streptococcus suis

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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