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- PDB-4h4r: Crystal Structure of Ferredoxin reductase, BphA4 E175C/Q177G muta... -

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Basic information

Entry
Database: PDB / ID: 4h4r
TitleCrystal Structure of Ferredoxin reductase, BphA4 E175C/Q177G mutant (oxidized form)
ComponentsBiphenyl dioxygenase ferredoxin reductase subunit
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / dioxygenase activity / nucleotide binding / cytoplasm
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)44,46213
Polymers43,1241
Non-polymers1,33812
Water6,377354
1
A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules

A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,92426
Polymers86,2482
Non-polymers2,67624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)98.456, 98.456, 170.721
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: 43124.137 Da / Num. of mol.: 1 / Mutation: E175C, 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.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2.5M Sodium formate, 0.1M acetate buffer, pH 5.4, 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: 0.98008 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 1.4→60.33 Å / Num. all: 95862 / Num. obs: 95862 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.85 Å2
Reflection shellResolution: 1.4→1.48 Å / % possible all: 100

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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→60.325 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8707 / SU ML: 0.12 / σ(F): 1.99 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 4793 5 %Random
Rwork0.1976 91069 --
obs0.1985 95862 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.06 Å2 / Biso mean: 17.0513 Å2 / Biso min: 5.93 Å2
Refinement stepCycle: LAST / Resolution: 1.4→60.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 89 354 3368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063072
X-RAY DIFFRACTIONf_angle_d1.1694190
X-RAY DIFFRACTIONf_chiral_restr0.071493
X-RAY DIFFRACTIONf_plane_restr0.005546
X-RAY DIFFRACTIONf_dihedral_angle_d13.9491081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.26021590.239230143173100
1.4159-1.43260.24881570.242130003157100
1.4326-1.450.22511580.225630093167100
1.45-1.46840.25441580.21929933151100
1.4684-1.48770.24711570.225429763133100
1.4877-1.50810.21821590.213330213180100
1.5081-1.52970.25441570.212429933150100
1.5297-1.55250.22691590.21330173176100
1.5525-1.57670.23241580.20430113169100
1.5767-1.60260.24521590.203430063165100
1.6026-1.63020.20531590.201130203179100
1.6302-1.65990.24991580.201730053163100
1.6599-1.69180.22181590.195830193178100
1.6918-1.72630.24371590.203330223181100
1.7263-1.76390.23471580.203530103168100
1.7639-1.80490.21561600.208130323192100
1.8049-1.85010.22621590.198530283187100
1.8501-1.90010.23671600.200630403200100
1.9001-1.9560.21921590.191430063165100
1.956-2.01910.19641600.194630553215100
2.0191-2.09130.2141610.18830473208100
2.0913-2.1750.20871600.19430503210100
2.175-2.2740.19471620.189530633225100
2.274-2.39390.20541610.193330593220100
2.3939-2.54390.22761610.196930713232100
2.5439-2.74030.21961630.20430943257100
2.7403-3.01610.2281630.210130903253100
3.0161-3.45250.19141650.191131243289100
3.4525-4.34960.19951610.17433091325297
4.3496-60.38140.20971640.19773103326792

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