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- PDB-1f3p: FERREDOXIN REDUCTASE (BPHA4)-NADH COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1f3p
TitleFERREDOXIN REDUCTASE (BPHA4)-NADH COMPLEX
ComponentsFERREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation 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 ...Reductase, C-terminal / Reductase C-terminal / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation 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 / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSenda, T. / Yamada, T. / Sakurai, N. / Kubota, M. / Nishizaki, T. / Masai, E. / Fukuda, M. / Mitsuidagger, Y.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase.
Authors: Senda, T. / Yamada, T. / Sakurai, N. / Kubota, M. / Nishizaki, T. / Masai, E. / Fukuda, M. / Mitsuidagger, Y.
#1: Journal: J.Bacteriol. / Year: 1994
Title: Identification of the bphA4 gene encoding ferredoxin reductase involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102.
Authors: Kikuchi, Y. / Nagata, Y. / Hinata, M. / Kimbara, K. / Fukuda, M. / Yano, Y. / Takagi, M.
History
DepositionJun 6, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FERREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6703
Polymers43,2211
Non-polymers1,4492
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.900, 98.900, 170.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly seems to be a dimer. However, the dimer form can not be indentified in the crystal.

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Components

#1: Protein FERREDOXIN REDUCTASE


Mass: 43221.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: KKS102 / Plasmid: PKH204 / Production host: Escherichia coli (E. coli)
References: UniProt: Q52437, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M Sodium formate, 100mM Na acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.4 / Details: Yamada, T., (2000) Protein Pept.Lett., 7, 277.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114.0 mg/mlprotein1drop
22.0 Msodium formate1reservoir
3100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→38 Å / Num. all: 133802 / Num. obs: 133802 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.478 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 19786 / Num. measured all: 133802

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.4→38 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction.
RfactorNum. reflectionSelection details
Rfree0.291 1592 Random
Rwork0.205 --
all0.213 16546 -
obs0.213 15752 -
Refinement stepCycle: LAST / Resolution: 2.4→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 97 81 3154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_torsion_deg1.4
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 38 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.4

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