5ZSQ | pdb_00005zsq

NifS from Hydrogenimonas thermophila, soaked with L-cysteine for 4 min

PDB DOI: https://doi.org/10.2210/pdb5ZSQ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Hydrogenimonas thermophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-29 Released: 2019-05-01
Deposition Author(s): Nakamura, R., Fujishiro, T., Takahashi, Y.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.245 (Depositor), 0.243 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZSQ

This is version 1.1 of the entry. See complete history.

Literature

X-ray snapshots of two classes of cysteine desulfurase enzymes NifS and SufS

Fujishiro, T., Nakamura, R., Takahashi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 92.58 kDa
Atom Count: 6,034
Modeled Residue Count: 774
Deposited Residue Count: 830
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A, B	415	Hydrogenimonas thermophila	Mutation(s): 0 Gene Names: SAMN05216234_11013 EC: 2.8.1.7
UniProt
Find proteins for A0A1I5NEH3 (Hydrogenimonas thermophila) Explore A0A1I5NEH3 Go to UniProtKB: A0A1I5NEH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1I5NEH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.245 (Depositor), 0.243 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.5	α = 90
b = 137.5	β = 90
c = 98.7	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17K14510
Japan Society for the Promotion of Science	Japan	15H04472

Revision History (Full details and data files)

Version 1.0: 2019-05-01
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.