1H1L | pdb_00001h1l

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.236 (Depositor), 0.219 (DCC)
R-Value Work:
0.176 (Depositor), 0.164 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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 Biological Chem 277: 35263

PubMed: 12133839 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M205888200
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 227.96 kDa
Atom Count: 17,025
Modeled Residue Count: 1,994
Deposited Residue Count: 2,000
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	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00466
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	519	Klebsiella pneumoniae	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P09772 (Klebsiella pneumoniae) Explore P09772 Go to UniProtKB: P09772
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09772
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFM Query on CFM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain N [auth C]	F [auth A], N [auth C]	FE-MO-S CLUSTER Fe₇ Mo S₉ UZRXIPMKRKMLQF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain N [auth C]
CLF Query on CLF Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain P [auth D] MOL2 format, chain I [auth B] MOL2 format, chain P [auth D] mmCIF format, chain I [auth B] mmCIF format, chain P [auth D]	I [auth B], P [auth D]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain P [auth D]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], M [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth D] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D]	J [auth B], O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain O [auth D] Interactions & Density Focus chain J [auth B] Focus chain O [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	G [auth A], H [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.236 (Depositor), 0.219 (DCC)
R-Value Work: 0.176 (Depositor), 0.164 (DCC)

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

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Entry History

Deposition Data

Released Date: 2002-07-29

Deposition Author(s):

Revision History (Full details and data files)

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