1N2C | pdb_00001n2c

NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE

PDB DOI: https://doi.org/10.2210/pdb1N2C/pdb

Classification: COMPLEX OF NITROGENASE PROTEINS
Organism(s): Azotobacter vinelandii
Mutation(s): No

Deposited: 1997-05-02 Released: 1997-11-12
Deposition Author(s): Schindelin, H., Kisker, C., Rees, D.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.238 (Depositor)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction.

Schindelin, H., Kisker, C., Schlessman, J.L., Howard, J.B., Rees, D.C.

(1997) Nature 387: 370-376

PubMed: 9163420 Search on PubMed
DOI: https://doi.org/10.1038/387370a0
Primary Citation Related Structures:
1N2C

PubMed Abstract:
The coupling of ATP hydrolysis to electron transfer by the enzyme nitrogenase during biological nitrogen fixation is an important example of a nucleotide-dependent transduction mechanism. The crystal structure has been determined for the complex between the Fe-protein and MoFe-protein components of nitrogenase stabilized by ADP x AIF4-, previously used as a nucleoside triphosphate analogue in nucleotide-switch proteins. The structure reveals that the dimeric Fe-protein has undergone substantial conformational changes. The beta-phosphate and AIF4- groups are stabilized through intersubunit contacts that are critical for catalysis and the redox centre is repositioned to facilitate electron transfer. Interactions in the nitrogenase complex have broad implications for signal and energy transduction mechanisms in multiprotein complexes.

Organizational Affiliation

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.

Macromolecule Content

Total Structure Weight: 361.25 kDa
Atom Count: 24,426
Modeled Residue Count: 3,096
Deposited Residue Count: 3,182
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROGENASE MOLYBDENUM-IRON PROTEIN	A, C	491	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	B, D	522	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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROGENASE IRON PROTEIN	E, F, G, H	289	Azotobacter vinelandii	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii) Explore P00459 Go to UniProtKB: P00459
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00459
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFM Query on CFM Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C]	J [auth A], N [auth C]	FE-MO-S CLUSTER Fe₇ Mo S₉ UZRXIPMKRKMLQF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth C]
CLF Query on CLF Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth D] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D]	L [auth B], P [auth D]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth D]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain W [auth F] SDF format, chain S [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain W [auth F] MOL2 format, chain S [auth E] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain W [auth F] mmCIF format, chain S [auth E]	AA [auth G], DA [auth H], S [auth E], W [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain S [auth E] Focus chain W [auth F]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain V [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain V [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain V [auth F]	V [auth F], Z [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain V [auth F] Focus chain Z [auth G]
HCA Query on HCA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C]	I [auth A], M [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C]
ALF Query on ALF Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain Y [auth G] SDF format, chain CA [auth H] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain CA [auth H] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain CA [auth H]	CA [auth H], R [auth E], U [auth F], Y [auth G]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain CA [auth H] Focus chain R [auth E] Focus chain U [auth F] Focus chain Y [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D]	K [auth B], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain O [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain X [auth G] SDF format, chain Q [auth E] SDF format, chain BA [auth H] MOL2 format, chain T [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Q [auth E] MOL2 format, chain BA [auth H] mmCIF format, chain T [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Q [auth E] mmCIF format, chain BA [auth H]	BA [auth H], Q [auth E], T [auth F], X [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain Q [auth E] Focus chain T [auth F] Focus chain X [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.238 (Depositor)
R-Value Work: 0.208 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 299.7	β = 90
c = 334.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1997-11-12

Deposition Author(s):

Schindelin, H.

Kisker, C.

Rees, D.C.

Revision History (Full details and data files)

Version 1.0: 1997-11-12
Type: Initial release
Version 1.1: 2008-03-10
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-11-20
Changes: Advisory, Derived calculations, Other
Version 1.4: 2021-07-21
Changes: Derived calculations, Refinement description
Version 1.5: 2023-08-09
Changes: Database references, Refinement description
Version 1.6: 2024-05-22
Changes: Data collection