5DBH | pdb_00005dbh

Crystal structure of O-acetylserine sulfhydrylase from haemophilus influenzae in complex with reaction intermediate alpha-aminoacrylate

PDB DOI: https://doi.org/10.2210/pdb5DBH/pdb
Entry: 5DBH supersedes: 4LHG

Classification: TRANSFERASE
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-21 Released: 2015-09-09
Deposition Author(s): Kaushik, A., Ekka, M.K., Singh, A.K., Kumaran, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.154 (Depositor), 0.158 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of O-acetylserine sulfhydrylase from haemophilus influenzae in complex with reaction intermediate alpha-aminoacrylate

Kaushik, A., Ekka, M.K., Singh, A.K., Kumaran, S.

To be published.

Macromolecule Content

Total Structure Weight: 34.66 kDa
Atom Count: 2,423
Modeled Residue Count: 312
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A [auth X]	322	Haemophilus influenzae Rd KW20	Mutation(s): 0 Gene Names: cysK, HI_1103 EC: 2.5.1.47
UniProt
Find proteins for P45040 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P45040 Go to UniProtKB: P45040
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45040
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0JO Query on 0JO Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid C₁₁ H₁₃ N₂ O₇ P BHIGINKEEFZJGX-YIXHJXPBSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.195 (Depositor), 0.198 (DCC)
R-Value Work: 0.154 (Depositor), 0.158 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.66	α = 90
b = 112.66	β = 90
c = 43.369	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

This entry supersedes: 4LHG

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2017-05-10
Changes: Non-polymer description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.