3U7Q | pdb_00003u7q

A. vinelandii nitrogenase MoFe protein at atomic resolution

PDB DOI: https://doi.org/10.2210/pdb3U7Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Azotobacter vinelandii
Mutation(s): No

Deposited: 2011-10-14 Released: 2011-12-07
Deposition Author(s): Spatzal, T., Einsle, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.146 (Depositor), 0.192 (DCC)
R-Value Work:
0.128 (Depositor)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Evidence for interstitial carbon in nitrogenase FeMo cofactor.

Spatzal, T., Aksoyoglu, M., Zhang, L., Andrade, S.L., Schleicher, E., Weber, S., Rees, D.C., Einsle, O.

(2011) Science 334: 940-940

PubMed: 22096190 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1214025
Primary Citation Related Structures:
3U7Q

PubMed Abstract:
The identity of the interstitial light atom in the center of the FeMo cofactor of nitrogenase has been enigmatic since its discovery. Atomic-resolution x-ray diffraction data and an electron spin echo envelope modulation (ESEEM) analysis now provide direct evidence that the ligand is a carbon species.

Organizational Affiliation

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 235.15 kDa
Atom Count: 18,955
Modeled Residue Count: 1,998
Deposited Residue Count: 2,030
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	492	Azotobacter vinelandii	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii) Explore P07328 Go to UniProtKB: P07328
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07328
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	523	Azotobacter vinelandii	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii) Explore P07329 Go to UniProtKB: P07329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07329
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICS Query on ICS Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain F [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain F [auth A]	F [auth A], Q [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain Q [auth C]
CLF Query on CLF Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain V [auth D] MOL2 format, chain K [auth B] MOL2 format, chain V [auth D] mmCIF format, chain K [auth B] mmCIF format, chain V [auth D]	K [auth B], V [auth D]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain V [auth D] Interactions & Density Focus chain K [auth B] Focus chain V [auth D]
1CL Query on 1CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain T [auth D] MOL2 format, chain J [auth B] MOL2 format, chain T [auth D] mmCIF format, chain J [auth B] mmCIF format, chain T [auth D]	J [auth B], T [auth D]	FE(8)-S(7) CLUSTER, OXIDIZED Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain T [auth D] Interactions & Density Focus chain J [auth B] Focus chain T [auth D]
HCA Query on HCA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain P [auth C]	E [auth A], P [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain E [auth A] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain P [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth D]	G [auth A] H [auth A] M [auth B] N [auth B] R [auth C] G [auth A], H [auth A], M [auth B], N [auth B], R [auth C], S [auth C], U [auth D], W [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B] mmCIF format, chain I [auth B] mmCIF format, chain L [auth B]	I [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth B] Interactions & Density Focus chain I [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain X [auth D] MOL2 format, chain O [auth B] MOL2 format, chain X [auth D] mmCIF format, chain O [auth B] mmCIF format, chain X [auth D]	O [auth B], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain X [auth D] Interactions & Density Focus chain O [auth B] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.146 (Depositor), 0.192 (DCC)
R-Value Work: 0.128 (Depositor)
R-Value Observed: 0.129 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.19	α = 90
b = 130.696	β = 110.67
c = 107.224	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Spatzal, T.

Einsle, O.

Revision History (Full details and data files)

Version 1.0: 2011-12-07
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 1.2: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description