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- PDB-1fp4: CRYSTAL STRUCTURE OF THE ALPHA-H195Q MUTANT OF NITROGENASE -

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Basic information

Entry
Database: PDB / ID: 1fp4
TitleCRYSTAL STRUCTURE OF THE ALPHA-H195Q MUTANT OF NITROGENASE
Components(NITROGENASE MOLYBDENUM-IRON PROTEIN ...) x 2
KeywordsOXIDOREDUCTASE / Iron-Sulfur-Molybdenum protein
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / 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 / FE-S CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSorlie, M. / Christiansen, J. / Lemon, B.J. / Peters, J.W. / Dean, D.R. / Hales, B.J.
CitationJournal: Biochemistry / Year: 2001
Title: Mechanistic features and structure of the nitrogenase alpha-Gln195 MoFe protein
Authors: Sorlie, M. / Christiansen, J. / Lemon, B.J. / Peters, J.W. / Dean, D.R. / Hales, B.J.
History
DepositionAug 30, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)233,22812
Polymers229,7784
Non-polymers3,4508
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32890 Å2
ΔGint-317 kcal/mol
Surface area56620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.200, 130.200, 80.400
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number4
Space group name H-MP1211

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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


Mass: 55353.027 Da / Num. of mol.: 2 / Mutation: H195Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN


Mass: 59535.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Non-polymers , 5 types, 441 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#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-CLP / FE-S CLUSTER


Mass: 703.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S8
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 298 K / Method: microcapillary batch diffusion / pH: 8
Details: PEG 4000, TRIS pH 8.0, sodium molybdate, microcapillary batch diffusion, temperature 298K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris11pH8.0
2350 mM11NaCl
330 %PEG40012
40.1 MTris12pH8.0
50.2 M12Na2MoO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 63058 / Num. obs: 59345 / % possible obs: 93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→20 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / % possible all: 70.9
Reflection
*PLUS
Num. obs: 63058 / % possible obs: 88.8 % / Num. measured all: 403283
Reflection shell
*PLUS
% possible obs: 60 % / Rmerge(I) obs: 0.252

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementResolution: 2.5→20 Å / σ(F): 1 / σ(I): 1
RfactorNum. reflectionSelection details
Rfree0.24 -random
Rwork0.184 --
all-63058 -
obs-59345 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15768 0 94 433 16295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.53
X-RAY DIFFRACTIONx_bond_d0.01
Refinement
*PLUS
Num. reflection Rfree: 2988 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.5

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