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- PDB-1m34: Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP... -

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Basic information

Entry
Database: PDB / ID: 1m34
TitleNitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate
Components
  • (Nitrogenase Molybdenum-Iron Protein ...) x 2
  • Nitrogenase Iron Protein 1
KeywordsOXIDOREDUCTASE / NITROGENASE / NITROGEN FIXATION / SIGNAL TRANSDUCTION / ELECTRON TRANSFER / ATP HYDROLYSIS / COMPLEX OF NITROGENASE PROTEINS
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchmid, B. / Einsle, O. / Chiu, H.-J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.C.
CitationJournal: Biochemistry / Year: 2002
Title: Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4 Stabilized structure
Authors: Schmid, B. / Einsle, O. / Chiu, H.-J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.C.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4Nov 20, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
E: Nitrogenase Iron Protein 1
F: Nitrogenase Iron Protein 1
G: Nitrogenase Iron Protein 1
H: Nitrogenase Iron Protein 1
I: Nitrogenase Molybdenum-Iron Protein alpha chain
J: Nitrogenase Molybdenum-Iron Protein beta chain
K: Nitrogenase Molybdenum-Iron Protein alpha chain
L: Nitrogenase Molybdenum-Iron Protein beta chain
M: Nitrogenase Iron Protein 1
N: Nitrogenase Iron Protein 1
O: Nitrogenase Iron Protein 1
P: Nitrogenase Iron Protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)722,49660
Polymers709,88216
Non-polymers12,61444
Water29,2561624
1
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
E: Nitrogenase Iron Protein 1
F: Nitrogenase Iron Protein 1
G: Nitrogenase Iron Protein 1
H: Nitrogenase Iron Protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,24830
Polymers354,9418
Non-polymers6,30722
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55400 Å2
ΔGint-446 kcal/mol
Surface area87950 Å2
MethodPISA
2
I: Nitrogenase Molybdenum-Iron Protein alpha chain
J: Nitrogenase Molybdenum-Iron Protein beta chain
K: Nitrogenase Molybdenum-Iron Protein alpha chain
L: Nitrogenase Molybdenum-Iron Protein beta chain
M: Nitrogenase Iron Protein 1
N: Nitrogenase Iron Protein 1
O: Nitrogenase Iron Protein 1
P: Nitrogenase Iron Protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,24830
Polymers354,9418
Non-polymers6,30722
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55440 Å2
ΔGint-443 kcal/mol
Surface area88370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)326.1, 75.8, 312.2
Angle α, β, γ (deg.)90.0, 102.6, 90.0
Int Tables number5
Space group name H-MC121
Details2:1 Complex Of Homodimeric Fe-Protein and Heterotetrameric Mofe-Protein. There are two complexes in the asymmetric unit

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Components

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Nitrogenase Molybdenum-Iron Protein ... , 2 types, 8 molecules ACIKBDJL

#1: Protein
Nitrogenase Molybdenum-Iron Protein alpha chain / NIFD / Nitrogenase MoFe protein alpha subunit / nitrogenase component I / dinitrogenase


Mass: 55231.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria)
References: UniProt: p07328, UniProt: P07328*PLUS, nitrogenase
#2: Protein
Nitrogenase Molybdenum-Iron Protein beta chain / NIFK / Nitrogenase MoFe protein beta subunit / nitrogenase component I / dinitrogenase


Mass: 59404.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria)
References: UniProt: p07329, UniProt: P07329*PLUS, nitrogenase

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Protein , 1 types, 8 molecules EFGHMNOP

#3: Protein
Nitrogenase Iron Protein 1 / NIFH / nitrogenase Fe protein alpha chain / Nitrogenase component II / Nitrogenase Fe protein 1 / ...NIFH / nitrogenase Fe protein alpha chain / Nitrogenase component II / Nitrogenase Fe protein 1 / Nitrogenase reductase


Mass: 31417.045 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria)
References: UniProt: p00459, UniProt: P00459*PLUS, nitrogenase

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Non-polymers , 9 types, 1668 molecules

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


Mass: 206.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical
ChemComp-CFM / FE-MO-S CLUSTER


Mass: 775.440 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe7MoS9
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8S7
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: AlF4
#10: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#11: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1624 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 296 K / Method: liquid diffusion / pH: 6.5
Details: PEG 8000, cacodylate, magnesium chloride, pH 6.5, LIQUID DIFFUSION, temperature 296.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein11
2100 mMMOPS/Tris11pH7.3
3100 mM11NaCl
45 mM11NaF
50.25 mM11AlCl3
61 mM11MgCl2
71 mM11Na2ATP
85 mM11Na2S2O4
9100 mMcacodylate-HCl12pH6.5
1030 mM12MgCl2
1119 %(w/w)PEG800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2001 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 273781 / Num. obs: 273781 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.34 Å / % possible all: 66.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 665961 / Rmerge(I) obs: 0.128
Reflection shell
*PLUS
% possible obs: 66.9 % / Rmerge(I) obs: 0.266

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 12963 random
Rwork0.2 --
all-259977 -
obs-259977 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48460 0 484 1624 50568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.63
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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