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- PDB-1h1l: NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, NIFV MUTANT -

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Basic information

Entry
Database: PDB / ID: 1h1l
TitleNITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, NIFV MUTANT
Components(NITROGENASE MOLYBDENUM IRON PROTEIN ...) x 2
KeywordsOXIDOREDUCTASE / BIOLOGICAL NITROGEN FIXATION / NITROGEN METABOLISM / MOLYBDOENZYMES / ELECTRON TRANSFER
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. ...Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / Nitrogenase molybdenum iron protein domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE-MO-S CLUSTER / CITRIC ACID / FE(8)-S(7) CLUSTER / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMayer, S.M. / Gormal, C.A. / Smith, B.E. / Lawson, D.M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: 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).
Authors: Mayer, S.M. / Gormal, C.A. / Smith, B.E. / Lawson, D.M.
History
DepositionJul 18, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAIN
B: NITROGENASE MOLYBDENUM IRON PROTEIN BETA CHAIN
C: NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAIN
D: NITROGENASE MOLYBDENUM IRON PROTEIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,96116
Polymers224,5154
Non-polymers3,44612
Water27,6891537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)204.060, 75.060, 164.260
Angle α, β, γ (deg.)90.00, 123.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99088, 0.02807, 0.1318), (0.02433, -0.92474, 0.37983), (0.13254, 0.37957, 0.91562)129.31363, -29.14841, -3.24961
2given(-0.99028, 0.02731, 0.13636), (0.02684, -0.92456, 0.38008), (0.13645, 0.38005, 0.91485)129.09775, -29.25258, -3.35041

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Components

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NITROGENASE MOLYBDENUM IRON PROTEIN ... , 2 types, 4 molecules ACBD

#1: Protein NITROGENASE MOLYBDENUM IRON PROTEIN ALPHA CHAIN / NITROGENASE COMPONENT I / DINITROGENASE


Mass: 53919.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CHAINS A AND C ARE ALPHA-SUBUNITS / Source: (natural) KLEBSIELLA PNEUMONIAE (bacteria) / Variant: NIFV MUTANT / Strain: UNF1613 / References: UniProt: P00466, nitrogenase
#2: Protein NITROGENASE MOLYBDENUM IRON PROTEIN BETA CHAIN / NITROGENASE COMPONENT I / DINITROGENASE


Mass: 58338.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CHAINS B AND D ARE BETA-SUBUNITS / Source: (natural) KLEBSIELLA PNEUMONIAE (bacteria) / Variant: NIFV MUTANT / Strain: UNF1613 / References: UniProt: P09772, nitrogenase

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Non-polymers , 6 types, 1549 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CFM / FE-MO-S CLUSTER


Mass: 775.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe7MoS9
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1537 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsNITROGEN FIXATION, CATALYZED BY THE NITROGENASE COMPLEX, THE IRON PROTEIN AND THE MOLYBDENUM-IRON ...NITROGEN FIXATION, CATALYZED BY THE NITROGENASE COMPLEX, THE IRON PROTEIN AND THE MOLYBDENUM-IRON PROTEIN COMPRISE TWO CATALYTIC COMPONENTS OF THE COMPLEX.
Sequence detailsN-TERMINAL SEQUENCING INDICATES THAT THE FIRST TWO AMINO ACIDS OF THE ALPHA SUBUNITS (CHAINS A AND ...N-TERMINAL SEQUENCING INDICATES THAT THE FIRST TWO AMINO ACIDS OF THE ALPHA SUBUNITS (CHAINS A AND C) ARE CLEAVED FROM THE PROTEIN. THUS RESIDUE 1 IN THE COORDINATE FILE CORRESPONDS TO RESIDUE 3 IN THE SWS ACCESSION NO. P00466. N-TERMINAL SEQUENCING INDICATES THAT THE FIRST AMINO ACID IN EACH OF THE BETA SUBUNITS (CHAINS B AND D) IS CLEAVED FROM THE PROTEIN. THUS RESIDUE 1 IN THE COORDINATE FILE CORRESPONDS TO RESIDUE 2 IN THE SWS ACCESSION NO. P09772.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46 %
Description: PRIOR TO DATA COLLECTION THE CRYSTAL WAS SOAKED FOR 5 MINS IN CRYOPROTECTANT (MOTHER LIQUOR WITH 25% ETHYLENE GLYCOL CONTAINING 20 MM SODIUM DITHIONITE (A REDUCTANT).
Crystal growMethod: liquid diffusion / pH: 7.4
Details: CRYSTALLIZED ANAEROBICALLY USING LIQUID-LIQUID DIFFUSION TECHNIQUE. FINAL CONCENTRATIONS AFTER EQUILIBRATION WERE: 7% (W/V) PEG6000, 0.4 - 0.6 M MGCL2, 50 MM TRIS-HCL PH 7.4, 1.3 MG/ML PROTEIN.
Crystal grow
*PLUS
Method: liquid-liquid diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM11NaCl
225 mMTris-HCl11pH7.4
310.1 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.936
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 154203 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.6 / % possible all: 85.2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å
Reflection shell
*PLUS
% possible obs: 85.2 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGU

1qgu


Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: TOWARDS THE END OF REFINEMENT ALL RESTRAIN WITHIN THE HETEROGENS CIT, CFM, AND CLF WERE EXPLICITL TURNED OFF. IN ADDITION, THE BONDS BETWEEN THESE HETEROGENS AND THE PROTEIN NOT RESTRAINED. ...Details: TOWARDS THE END OF REFINEMENT ALL RESTRAIN WITHIN THE HETEROGENS CIT, CFM, AND CLF WERE EXPLICITL TURNED OFF. IN ADDITION, THE BONDS BETWEEN THESE HETEROGENS AND THE PROTEIN NOT RESTRAINED. BOTH CITRATE MOLECULES WERE REFINED WITH AN OCCUPANCY OF 0.5. A NETWORK OF WATER MOLECULES WAS THOU TO BE PRESENT IN ITS ABSENCE. THREE WATERS WERE MODELLED IN PLA EACH CITRATE AND GIVEN OCCUPANCIES OF 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 7646 5 %RANDOM
Rwork0.176 ---
obs-154203 94.2 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15392 0 96 1537 17025
Refinement
*PLUS
Highest resolution: 1.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d0.034

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