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- PDB-2yvj: Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-B... -

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Basic information

Entry
Database: PDB / ID: 2yvj
TitleCrystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex
Components
  • Biphenyl dioxygenase ferredoxin subunit
  • Ferredoxin reductase
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / electron transfer / ferredoxin / ferredoxin reductase / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / catabolic process / 2 iron, 2 sulfur cluster binding / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / : / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain ...Reductase, C-terminal / Reductase C-terminal / : / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Ferredoxin reductase / Biphenyl dioxygenase ferredoxin subunit
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSenda, T. / Senda, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin
Authors: Senda, M. / Kishigami, S. / Kimura, S. / Fukuda, M. / Ishida, T. / Senda, T.
History
DepositionApr 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_dist_value / _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_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: Ferredoxin reductase
B: Biphenyl dioxygenase ferredoxin subunit
P: Ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4478
Polymers98,3693
Non-polymers3,0785
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.596, 173.715, 60.976
Angle α, β, γ (deg.)90.00, 115.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 3 molecules APB

#1: Protein Ferredoxin reductase / ferredoxin reductase BPHA4


Mass: 43221.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: strain KKS102 / Gene: bphA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52437, ferredoxin-NADP+ reductase
#2: Protein Biphenyl dioxygenase ferredoxin subunit


Mass: 11926.499 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: strain KKS102 / Gene: bphA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52440

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Non-polymers , 4 types, 83 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 30%(W/V) PEG4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→18 Å / Num. obs: 86196 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.18
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 5.46 / % possible all: 93.3

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Processing

Software
NameClassification
MOLREPphasing
SHELXL-97refinement
ADSCdata collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Num. parameters: 28196 / Num. restraintsaints: 29665 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE CRYSTAL FORM IS TWINNED BY THE OPERATOR L,-K,H, PERFECT TWINED CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 4047 5 %RANDOM
all0.183 85677 --
obs0.1789 85677 92.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7044.4
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 180 78 7045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0267
X-RAY DIFFRACTIONs_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.12
X-RAY DIFFRACTIONs_approx_iso_adps0

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