7MCI | pdb_00007mci

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 (Depositor), 0.194 (DCC)
R-Value Work:
0.172 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (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 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
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 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% 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 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% 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 (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] mmCIF format, chain F [auth A] mmCIF 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] mmCIF format, chain K [auth B] mmCIF 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] mmCIF format, chain E [auth A] mmCIF 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 H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF 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 CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [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 CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [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] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF 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] mmCIF format, chain Q [auth B] mmCIF 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] mmCIF format, chain G [auth A] mmCIF 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 (Depositor), 0.194 (DCC)
R-Value Work: 0.172 (Depositor), 0.171 (DCC)
R-Value Observed: 0.173 (Depositor)

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

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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