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- PDB-1de0: MODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE ... -

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Basic information

Entry
Database: PDB / ID: 1de0
TitleMODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE NITROGENASE FE PROTEIN
ComponentsNITROGENASE IRON PROTEIN
KeywordsOXIDOREDUCTASE / REDOX PROTEINS / [FES] CLUSTERS / FE 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 / Resolution: 2.4 Å
AuthorsJang, S.B. / Seefeldt, L.C. / Peters, J.W.
Citation
Journal: Biochemistry / Year: 2000
Title: Modulating the midpoint potential of the [4Fe-4S] cluster of the nitrogenase Fe protein.
Authors: Jang, S.B. / Seefeldt, L.C. / Peters, J.W.
#1: Journal: Science / Year: 1992
Title: Crystallographic Structure of the Nitrogenase Iron Protein from Azotobacter vinelandii
Authors: Georgiadis, M.M. / Komiya, H. / Chakrabarti, 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.
#3: Journal: Nature / Year: 1997
Title: Structure of ADP x AlF4(-)-stabilized Nitrogenase Complex and its Implications for Signal Transduction
Authors: Schindelin, H. / Kisker, C. / Schlessman, J.L. / Howard, J.B. / Rees, D.C.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: 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 3, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)63,2643
Polymers62,9122
Non-polymers3521
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-34 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.54, 91.05, 63.35
Angle α, β, γ (deg.)90, 99.76, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NITROGENASE IRON PROTEIN


Mass: 31456.084 Da / Num. of mol.: 2 / Mutation: F135W / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / 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.: 224 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 8.5
Details: PEG 4000, 0.1 M TRIS HCL, 0.2 M SODIUM ACETATE, pH 8.5, SMALL TUBES, temperature 277K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG400011
20.1 MTris-HCl11
30.2 Msodium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 265157 / Num. obs: 24852 / % possible obs: 9.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 18.4 / Redundancy: 6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6 % / Rmerge(I) obs: 0.253 / % possible all: 0.2
Reflection
*PLUS
% possible obs: 95.2 % / Num. measured all: 265157
Reflection shell
*PLUS
% possible obs: 75.5 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2.4→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.281 1152 5
Rwork0.221 --
obs0.221 22802 -
all-265157 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 8 224 4612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.3 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.576

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