1H1L

NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, NIFV MUTANT

• PDB DOI: https://doi.org/10.2210/pdb1H1L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Mutation(s): No 


• Deposited: 2002-07-18 Released: 2002-07-29 
• Deposition Author(s): Mayer, S.M., Gormal, C.A., Smith, B.E., Lawson, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.176 

Starting Model: experimental

Literature

Crystallographic Analysis of the Mofe Protein of Nitrogenase from a Nifv Mutant of Klebsiella Pneumoniae Identifies Citrate as a Ligand to the Molybdenum of Iron Molybdenum Cofactor (Femoco).

Mayer, S.M., Gormal, C.A., Smith, B.E., Lawson, D.M.

(2002) J Biol Chem 277: 35263

• PubMed: 12133839 
• DOI: https://doi.org/10.1074/jbc.M205888200
• Primary Citation of Related Structures:  
  1H1L


• PubMed Abstract: 
  

  The x-ray crystal structure of NifV(-) Klebsiella pneumoniae nitrogenase MoFe protein (NifV(-) Kp1) has been determined and refined to a resolution of 1.9 A. This is the first structure for a nitrogenase MoFe protein with an altered cofactor. Moreover, it is the first direct evidence that the organic acid citrate is not just present, but replaces homocitrate as a ligand to the molybdenum atom of the iron molybdenum cofactor (FeMoco). Subsequent refinement of the structure revealed that the citrate was present at reduced occupancy.

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Organizational Affiliation: 

Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 227.96 kDa 
• Atom Count: 17,025 
• Modelled Residue Count: 1,994 
• Deposited Residue Count: 2,000 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAIN	A, C	481	Klebsiella pneumoniae	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P00466 (Klebsiella pneumoniae) Explore P00466  Go to UniProtKB:  P00466

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROGENASE MOLYBDENUM IRON PROTEIN BETA CHAIN	B, D	519	Klebsiella pneumoniae	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for P09772 (Klebsiella pneumoniae) Explore P09772  Go to UniProtKB:  P09772

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CFM	F [auth A], N [auth C]	FE-MO-S CLUSTER Fe7 Mo S9 UZRXIPMKRKMLQF-UHFFFAOYSA-N
CLF	I [auth B], P [auth D]	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-UHFFFAOYSA-N
CIT	E [auth A], M [auth C]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CL	J [auth B], O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], H [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.06	α = 90
b = 75.06	β = 123.95
c = 164.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-29 
Deposition Author(s): Mayer, S.M., Gormal, C.A., Smith, B.E., Lawson, D.M.

Revision History  

• Version 1.0: 2002-07-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-24
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description