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- PDB-4h4t: Crystal Structure of Ferredoxin reductase, BphA4 T176R mutant (ox... -

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Basic information

Entry
Database: PDB / ID: 4h4t
TitleCrystal Structure of Ferredoxin reductase, BphA4 T176R mutant (oxidized form)
ComponentsBiphenyl dioxygenase ferredoxin reductase subunit
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


dioxygenase activity / flavin adenine dinucleotide 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 / 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 / FORMIC ACID / Biphenyl dioxygenase ferredoxin reductase subunit
Similarity search - Component
Biological speciesAcidovorax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)44,70715
Polymers43,2771
Non-polymers1,43014
Water7,152397
1
A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules

A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,41430
Polymers86,5552
Non-polymers2,86028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area9370 Å2
ΔGint-26 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.332, 98.332, 170.423
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: 43277.273 Da / Num. of mol.: 1 / Mutation: T176R
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 / 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 / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 397 / 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: 55.24 %
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: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→85.16 Å / Num. all: 77482 / Num. obs: 77482 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.6 Å2
Reflection shellResolution: 1.5→1.58 Å / % possible all: 98.6

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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: 1.5→76.177 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8703 / SU ML: 0.14 / σ(F): 1.99 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 3876 5 %Random
Rwork0.186 73603 --
obs0.187 77479 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.54 Å2 / Biso mean: 17.3861 Å2 / Biso min: 6.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→76.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 95 397 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063134
X-RAY DIFFRACTIONf_angle_d1.154272
X-RAY DIFFRACTIONf_chiral_restr0.071498
X-RAY DIFFRACTIONf_plane_restr0.005558
X-RAY DIFFRACTIONf_dihedral_angle_d14.1481129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51830.26551370.21992566270399
1.5183-1.53750.26911360.21872592272898
1.5375-1.55770.22661350.21212573270899
1.5577-1.57910.25781340.20842565269999
1.5791-1.60170.26241360.20712570270699
1.6017-1.62560.24411360.19842586272299
1.6256-1.6510.23981360.1972572270899
1.651-1.6780.24061370.20542600273799
1.678-1.7070.25431380.19812593273199
1.707-1.7380.22451370.19512612274999
1.738-1.77140.23781370.1962598273599
1.7714-1.80760.24991360.20232597273399
1.8076-1.84690.22811360.20032600273699
1.8469-1.88990.23671380.19812619275799
1.8899-1.93710.19551380.19342608274699
1.9371-1.98950.22321370.189226092746100
1.9895-2.04810.21441410.18726782819100
2.0481-2.11420.18181370.184826062743100
2.1142-2.18970.21751390.185326562795100
2.1897-2.27740.21461390.181826132752100
2.2774-2.38110.2011390.185326632802100
2.3811-2.50660.19511410.185626812822100
2.5066-2.66370.22761410.192526642805100
2.6637-2.86940.20691410.193826772818100
2.8694-3.15810.19151420.193427092851100
3.1581-3.61510.18031440.164727272871100
3.6151-4.55460.16951430.15612712285598
4.5546-76.27560.18861450.18522757290293

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