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- PDB-1g1m: ALL-FERROUS NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII -

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Basic information

Entry
Database: PDB / ID: 1g1m
TitleALL-FERROUS NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII
ComponentsNITROGENASE IRON PROTEIN
KeywordsOXIDOREDUCTASE / IRON PROTEIN / NITROGENASE / ALL-FERROUS
Function / homology
Function and homology information


nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
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. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...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. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Nitrogenase iron protein 1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsStrop, P. / Takahara, P.M. / Chiu, H.-J. / Angove, H.C. / Burgess, B.K. / Rees, D.C.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of the all-ferrous [4Fe-4S]0 form of the nitrogenase iron protein from Azotobacter vinelandii.
Authors: Strop, P. / Takahara, P.M. / Chiu, H. / Angove, H.C. / Burgess, B.K. / Rees, D.C.
History
DepositionOct 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: NITROGENASE IRON PROTEIN
B: NITROGENASE IRON PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1863
Polymers62,8342
Non-polymers3521
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-36 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.0, 93.3, 62.8
Angle α, β, γ (deg.)90, 98.9, 90
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein NITROGENASE IRON PROTEIN / E.C.1.18.6.1 / NITROGENASE COMPONENT II / NITROGENASE REDUCTASE / NIFH / NITROGENASE FE PROTEIN


Mass: 31417.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Cell line: NIFH / References: UniProt: P00459, nitrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 295 K / pH: 8
Details: 26-29% PEG 4000, 700-900 mM NaCl, 100 mM Tris (pH 8.0), 20% glycerol, capillary microbatch method at 295 K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
126-29 %PEG400011
2700-900 mM11NaCl
3100 mMTris11
430 mg/mlprotein12
520 %glycerol12
6450 mM12NaCl
750 mMTris12

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 28724 / % possible obs: 93.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.3
Reflection shellResolution: 2.25→2.39 Å / Rmerge(I) obs: 0.319 / % possible all: 87
Reflection
*PLUS
Num. measured all: 154673
Reflection shell
*PLUS
Lowest resolution: 2.33 Å / % possible obs: 85.2 % / Rmerge(I) obs: 0.306

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1480 5 %random
Rwork0.238 ---
obs-28765 --
Refinement stepCycle: LAST / Resolution: 2.25→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 8 348 4713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.95
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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