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- PDB-4h4v: Crystal Structure of Ferredoxin reductase, BphA4 E175C/T176R/Q177... -

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Basic information

Entry
Database: PDB / ID: 4h4v
TitleCrystal Structure of Ferredoxin reductase, BphA4 E175C/T176R/Q177G mutant (oxidized form)
ComponentsBiphenyl dioxygenase ferredoxin reductase subunit
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


dioxygenase activity / nucleotide binding
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 ...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 / FORMIC ACID / Biphenyl dioxygenase ferredoxin reductase subunit
Similarity search - Component
Biological speciesAcidovorax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNishizawa, A. / Harada, A. / Senda, M. / Tachihara, Y. / Muramatsu, D. / Kishigami, S. / Mori, S. / Sugiyama, K. / Senda, T. / Kimura, S.
CitationJournal: To be Published
Title: Random Mutagenesis with the Project Assessment for Complete Conversion of Co-Factor Specificity of a Ferredoxin Reductase BphA4
Authors: Nishizawa, A. / Harada, A. / Senda, M. / Tachihara, Y. / Muramatsu, D. / Kishigami, S. / Mori, S. / Sugiyama, K. / Senda, T. / Kimura, S.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,61015
Polymers43,1801
Non-polymers1,43014
Water8,467470
1
A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules

A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,22030
Polymers86,3602
Non-polymers2,86028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)98.296, 98.296, 170.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Biphenyl dioxygenase ferredoxin reductase subunit


Mass: 43180.227 Da / Num. of mol.: 1 / Mutation: E175C, T176R, Q177G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax (bacteria) / Strain: KKS102 / Gene: bphA4 / Production host: Escherichia coli (E. coli) / References: UniProt: E7FJB9, ferredoxin-NAD+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 2.5M Sodium formate, 0.1M acetate buffer, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→85.13 Å / Num. all: 95724 / Num. obs: 95724 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.24 Å2
Reflection shellResolution: 1.4→1.48 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GQW

2gqw


Resolution: 1.4→47.221 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8813 / SU ML: 0.11 / σ(F): 2.01 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 4785 5 %Random
Rwork0.1834 90933 --
obs0.1843 95718 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.09 Å2 / Biso mean: 16.4012 Å2 / Biso min: 5.18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 95 470 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063103
X-RAY DIFFRACTIONf_angle_d1.1874237
X-RAY DIFFRACTIONf_chiral_restr0.072497
X-RAY DIFFRACTIONf_plane_restr0.006555
X-RAY DIFFRACTIONf_dihedral_angle_d13.8831096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.3999-1.41580.24841550.215729443099
1.4158-1.43250.25271580.211829953153
1.4325-1.44990.24231560.205129703126
1.4499-1.46830.25271590.198730093168
1.4683-1.48760.21341570.198229843141
1.4876-1.5080.20891560.193429763132
1.508-1.52950.20631580.191529693127
1.5295-1.55240.22031560.19629783134
1.5524-1.57660.21521590.188130173176
1.5766-1.60250.21541550.188329633118
1.6025-1.63010.2091580.17830013159
1.6301-1.65980.19721580.185130073165
1.6598-1.69170.2021590.178130063165
1.6917-1.72620.21151580.184230063164
1.7262-1.76380.23431580.189829973155
1.7638-1.80480.22011580.190330013159
1.8048-1.84990.21531590.188230383197
1.8499-1.89990.20911580.187429973155
1.8999-1.95580.22131600.183130263186
1.9558-2.0190.19781580.184630173175
2.019-2.09110.21631600.178330443204
2.0911-2.17490.21141600.181630303190
2.1749-2.27380.21281600.173630333193
2.2738-2.39370.17221600.180930563216
2.3937-2.54370.22211610.18430483209
2.5437-2.74010.22151620.191830883250
2.7401-3.01580.19921630.197630883251
3.0158-3.4520.19551640.180931133277
3.452-4.34870.17041660.161131683334
4.3487-47.24790.17651760.180833643540

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