7MCI

MoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor

PDB DOI: https://doi.org/10.2210/pdb7MCI/pdb

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

Deposited: 2021-04-02 Released: 2022-05-18
Deposition Author(s): Kang, W., Lee, C., Hu, Y., Ribbe, M.W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.195
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Evidence of substrate binding and product release via belt-sulfur mobilization of the nitrogenase cofactor

Lee, C.C., Kang, W., Jasniewski, A.J., Stiebritz, M.T., Tanifuji, K., Ribbe, M.W., Hu, Y.

(2022) Nat Catal 5: 443-454

DOI: https://doi.org/10.1038/s41929-022-00782-7

Macromolecule Content

Total Structure Weight: 234.86 kDa
Atom Count: 17,333
Modelled Residue Count: 1,998
Deposited Residue Count: 2,030
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	492	Azotobacter vinelandii DJ	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07328
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	523	Azotobacter vinelandii DJ	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 (Subject of Investigation/LOI) Query on ICS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C]	F [auth A], S [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain S [auth C]
CLF (Subject of Investigation/LOI) Query on CLF Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain T [auth C] MOL2 format, chain K [auth B] MOL2 format, chain T [auth C]	K [auth B], T [auth C]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain T [auth C] Interactions & Density Focus chain K [auth B] Focus chain T [auth C]
HCA (Subject of Investigation/LOI) Query on HCA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain R [auth C]	E [auth A], R [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain E [auth A] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain R [auth C]
MO Query on MO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain X [auth C] MOL2 format, chain I [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain X [auth C]	H [auth A] I [auth A] J [auth A] V [auth C] W [auth C] H [auth A], I [auth A], J [auth A], V [auth C], W [auth C], X [auth C]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain EA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain Y [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D]	Q [auth B], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain Y [auth D] Interactions & Density Focus chain Q [auth B] Focus chain Y [auth D]
H2S Query on H2S Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain U [auth C]	G [auth A], U [auth C]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.195
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.834	α = 90
b = 73.995	β = 103.051
c = 208.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM67626
Department of Energy (DOE, United States)	United States	DE-SC0016510