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- PDB-1n2c: NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP... -

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Basic information

Entry
Database: PDB / ID: 1n2c
TitleNITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE
Components
  • (NITROGENASE MOLYBDENUM-IRON ...) x 2
  • NITROGENASE IRON PROTEIN
KeywordsCOMPLEX OF NITROGENASE PROTEINS / NITROGENASE / NITROGEN FIXATION / SIGNAL TRANSDUCTION / ELECTRON TRANSFER / ATP HYDROLYSIS
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 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 iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / Nitrogenase molybdenum-iron protein beta chain, N-terminal ...Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / FE-MO-S CLUSTER / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / IRON/SULFUR CLUSTER / Nitrogenase iron protein 1 / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchindelin, H. / Kisker, C. / Rees, D.C.
CitationJournal: Nature / Year: 1997
Title: Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction.
Authors: Schindelin, H. / Kisker, C. / Schlessman, J.L. / Howard, J.B. / Rees, D.C.
History
DepositionMay 2, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 21, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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 / _refine.ls_percent_reflns_obs / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6May 22, 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
B: NITROGENASE MOLYBDENUM-IRON PROTEIN
C: NITROGENASE MOLYBDENUM-IRON PROTEIN
D: NITROGENASE MOLYBDENUM-IRON PROTEIN
E: NITROGENASE IRON PROTEIN
F: NITROGENASE IRON PROTEIN
G: NITROGENASE IRON PROTEIN
H: NITROGENASE IRON PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,24830
Polymers354,9418
Non-polymers6,30722
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55490 Å2
ΔGint-452 kcal/mol
Surface area84850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 299.700, 334.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.983345, -0.051886, 0.174183), (-0.056575, -0.823381, -0.564662), (0.172717, -0.565112, 0.806733)5.04319, 180.69858, 56.00419
2given(-0.982758, -0.052821, 0.177192), (-0.057545, -0.823353, -0.564605), (0.175714, -0.565066, 0.806117)4.97166, 180.73842, 55.99032
3given(-0.880435, -0.467672, -0.078211), (-0.467474, 0.828502, 0.308307), (-0.079389, 0.308006, -0.948066)75.99072, 9.53609, 59.00141
4given(-0.979867, -0.06144, 0.18996), (-0.057419, -0.824547, -0.562872), (0.191214, -0.562447, 0.804419)5.27959, 180.66811, 56.00768
5given(0.875998, 0.466879, -0.121043), (0.481281, -0.829724, 0.282712), (0.03156, -0.305911, -0.951537)-58.78347, 135.23579, 112.32442

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Components

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

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


Mass: 55231.848 Da / Num. of mol.: 2
Fragment: CHAINS A AND C ARE THE ALPHA CHAINS, CHAINS B AND D ARE THE BETA CHAINS
Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein NITROGENASE MOLYBDENUM-IRON PROTEIN / NITROGENASE COMPONENT I / DINITROGENASE


Mass: 59404.684 Da / Num. of mol.: 2
Fragment: CHAINS A AND C ARE THE ALPHA CHAINS, CHAINS B AND D ARE THE BETA CHAINS
Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

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Protein , 1 types, 4 molecules EFGH

#3: Protein
NITROGENASE IRON PROTEIN / NITROGENASE COMPONENT II / NITROGENASE REDUCTASE


Mass: 31417.045 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: 2\:1 COMPLEX OF HOMODIMERIC FE-PROTEIN AND HETEROTETRAMERIC MOFE-PROTEIN
Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

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Non-polymers , 8 types, 22 molecules

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


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical ChemComp-CFM / FE-MO-S CLUSTER


Mass: 775.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe7MoS9
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#10: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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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: 2.8 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 6.5
Details: 16-20% PEG 8000, 0.1 M CACODYLATE PH 6.5 AND 20-50 MM MGCL2
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 %PEG800011
20.1 Mcacodylate11
320-50 mM11MgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 57735 / % possible obs: 73.8 % / Redundancy: 1.8 % / Rsym value: 0.098 / Net I/σ(I): 9.8
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.245 / % possible all: 28.8
Reflection
*PLUS
Num. measured all: 104037 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 28.8 % / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIN

1min
PDB Unreleased entry


Resolution: 3→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: ONE B-FACTOR PER RESIDUE / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -2 %RANDOM IN THIN SHELLS
Rwork0.208 ---
obs0.208 57735 73.8 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24190 0 142 0 24332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.12
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.011500
22X-RAY DIFFRACTION0.011500
33X-RAY DIFFRACTION0.011500
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

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