5ZSS | pdb_00005zss

L-Cysteine-PLP reaction intermediate of NifS from Hydrogenimonas thermophila

PDB DOI: https://doi.org/10.2210/pdb5ZSS/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, T., Fujishiro, T., Takahashi, Y.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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

To be published.

Macromolecule Content

Total Structure Weight: 92.7 kDa
Atom Count: 6,029
Modeled Residue Count: 773
Deposited Residue Count: 830
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1I5NEH3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1I5NEH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C6P Query on C6P Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE C₁₁ H₁₇ N₂ O₇ P S FPVGQJHHLSVHOT-VIFPVBQESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.2	α = 90
b = 138.2	β = 90
c = 99.1	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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 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.