7CNV | pdb_00007cnv

Crystal structure of IscU H106C variant

PDB DOI: https://doi.org/10.2210/pdb7CNV/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Methanothrix thermoacetophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-08-03 Released: 2021-08-04
Deposition Author(s): Kunichika, K., Takahashi, Y., Fujishiro, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.233 (Depositor), 0.232 (DCC)
R-Value Work:
0.210 (Depositor), 0.209 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7CNV

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

Literature

[2Fe-2S] clusters-assembled dimeric structures of IscU iron-sulfur scaffold

Kunichika, K., Fujishiro, T., Takahashi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 89.33 kDa
Atom Count: 5,983
Modeled Residue Count: 768
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen-fixing NifU domain protein	A, B, C, D, E A, B, C, D, E, F	132	Methanothrix thermoacetophila	Mutation(s): 1
UniProt
Find proteins for A0B757 (Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT)) Explore A0B757 Go to UniProtKB: A0B757
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0B757
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] N [auth C] R [auth D] T [auth E] G [auth A], J [auth B], N [auth C], R [auth D], T [auth E], W [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] O [auth C] P [auth C] H [auth A], I [auth A], K [auth B], O [auth C], P [auth C], S [auth D], U [auth E], V [auth E], X [auth F], Y [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.233 (Depositor), 0.232 (DCC)
R-Value Work: 0.210 (Depositor), 0.209 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.82	α = 90
b = 104.08	β = 106.12
c = 65.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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: 2021-08-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K14510

Revision History (Full details and data files)

Version 1.0: 2021-08-04
Type: Initial release
Version 1.1: 2023-11-29
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.