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- PDB-1g5p: NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII -

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Basic information

Entry
Database: PDB / ID: 1g5p
TitleNITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII
ComponentsNITROGENASE IRON PROTEIN
KeywordsOXIDOREDUCTASE / IRON PROTEIN
Function / homology
Function and homology information


nitrogenase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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: 2.2 Å
AuthorsStrop, P. / Takahara, P.M. / Chiu, H.J. / Angove, H.C. / Burgess, B.K. / Rees, D.C.
Citation
Journal: 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.
#1: Journal: Science / Year: 1992
Title: Crystallographic Structure of the Nitrogenase Iron Protein from Azotobacter vinelandii
Authors: KOMIYA, H. / GEORGIADIS, M.M. / CHAKRABARTI, P.P. / WOO, D. / KORNUC, J.J. / REES, D.C.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: CONFORMATIONAL VARIABILITY IN STRUCTURES OF THE NITROGENASE IRON PROTEINS FROM AZOTOBACTER VINELANDII AND CLOSTRIDIUM PASTEURIANUM
Authors: SCHLESSMAN, J.L. / WOO, D. / JOSHUA-TOR, L. / HOWARD, J.B. / REES, D.C.
History
DepositionNov 1, 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 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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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
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-38 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.120, 90.530, 91.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NITROGENASE IRON PROTEIN


Mass: 31417.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GENE: NIFH / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: OP / References: UniProt: P00459, nitrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 8
Details: 25-30% PEG 4000, 140-200 mM NA2MOO4, 100 mM TRIS-CL, PH 8.0; PROTEIN WAS IN 20% GLYCEROL, 50 mM TRIS-CL, PH 8.0, 450 mM NACL, AND 2 mM NA2S2O4 , LIQUID DIFFUSION, temperature 298K
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 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1995
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 29060 / % possible obs: 92.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.309 / % possible all: 94.9

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NIP

1nip


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 1737 RANDOM
Rwork0.223 --
obs-29180 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 8 351 4707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_deg1.7
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.336 185 -
Rwork0.295 --
obs-2747 94.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Rfactor Rfree: 0.336 / Rfactor Rwork: 0.295

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