5VPR | pdb_00005vpr

Crystal Structure of Cysteine desulfurase from Elizabethkingia anophelis with covalently bound pyridoxal phosphate

PDB DOI: https://doi.org/10.2210/pdb5VPR/pdb

Classification: TRANSFERASE
Organism(s): Elizabethkingia anophelis NUHP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-05-05 Released: 2017-05-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.204 (Depositor), 0.205 (DCC)
R-Value Work:
0.170 (Depositor), 0.172 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Cysteine desulfurase from Elizabethkingia anophelis with covalently bound pyridoxal phosphate

Dranow, D.M., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 46.47 kDa
Atom Count: 2,890
Modeled Residue Count: 366
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A	414	Elizabethkingia anophelis NUHP1	Mutation(s): 0 Gene Names: BD94_3973 EC: 2.8.1.7
UniProt
Find proteins for A0A077EMQ8 (Elizabethkingia anophelis NUHP1) Explore A0A077EMQ8 Go to UniProtKB: A0A077EMQ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077EMQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.204 (Depositor), 0.205 (DCC)
R-Value Work: 0.170 (Depositor), 0.172 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.18	α = 90
b = 82.04	β = 99.44
c = 70.12	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2017-10-11
Changes: Data collection
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection

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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.