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- PDB-1b0v: I40N MUTANT OF AZOTOBACTER VINELANDII FDI -

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Basic information

Entry
Database: PDB / ID: 1b0v
TitleI40N MUTANT OF AZOTOBACTER VINELANDII FDI
ComponentsPROTEIN (FERREDOXIN)
KeywordsELECTRON TRANSPORT / IRON-SULFUR
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding
Similarity search - Function
Ferredoxin, C-terminal / Domain of unknown function (DUF3470) / 7Fe ferredoxin / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits ...Ferredoxin, C-terminal / Domain of unknown function (DUF3470) / 7Fe ferredoxin / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / IRON/SULFUR CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSridhar, V. / Prasad, G.S. / Stout, C.D. / Chen, K. / Burgess, B.K.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I.
Authors: Chen, K. / Tilley, G.J. / Sridhar, V. / Prasad, G.S. / Stout, C.D. / Armstrong, F.A. / Burgess, B.K.
History
DepositionNov 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _diffrn_source.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0Nov 3, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 3.1Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FERREDOXIN)
B: PROTEIN (FERREDOXIN)
C: PROTEIN (FERREDOXIN)
D: PROTEIN (FERREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,83212
Polymers48,2424
Non-polymers2,5908
Water00
1
A: PROTEIN (FERREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7083
Polymers12,0601
Non-polymers6472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (FERREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7083
Polymers12,0601
Non-polymers6472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (FERREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7083
Polymers12,0601
Non-polymers6472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (FERREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7083
Polymers12,0601
Non-polymers6472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.000, 55.300, 62.300
Angle α, β, γ (deg.)78.10, 85.20, 71.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PROTEIN (FERREDOXIN)


Mass: 12060.476 Da / Num. of mol.: 4 / Mutation: I40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: JG100 / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P00214
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
Compound details4 COPIES OF I40N FDI IN THE ASYMMETRIC UNIT, EACH WITH A DIFFERENT CONFORMATION OF ASN40. THIS ...4 COPIES OF I40N FDI IN THE ASYMMETRIC UNIT, EACH WITH A DIFFERENT CONFORMATION OF ASN40. THIS AMINO ACID REPLACEMENT AFFECT THE REDUCTION POTENTIAL OF THE [4FE-4S]2+/+ CLUSTER.

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: Shen, B., (1994) J. Biol. Chem., 269, 8564.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
20.5 Mpotassium phosphate1drop
31.2 Mammonium sulfate1drop
43.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 11184 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rsym value: 0.165 / Net I/σ(I): 3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.2 / % possible all: 53
Reflection
*PLUS
Num. obs: 11182 / Num. measured all: 17912 / Rmerge(I) obs: 0.165
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.43

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FD1

6fd1


Resolution: 2.8→20 Å / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.209 --
obs-11140 87.3 %
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 60 0 3424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.5
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: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.83
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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