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- PDB-4h4p: Crystal Structure of Ferredoxin reductase, BphA4 E175Q/Q177K muta... -

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Basic information

Entry
Database: PDB / ID: 4h4p
TitleCrystal Structure of Ferredoxin reductase, BphA4 E175Q/Q177K 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: 1.502 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)44,46711
Polymers43,2211
Non-polymers1,24610
Water4,684260
1
A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules

A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,93422
Polymers86,4432
Non-polymers2,49220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Unit cell
Length a, b, c (Å)98.402, 98.402, 170.577
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: 43221.250 Da / Num. of mol.: 1 / Mutation: E175Q, Q177K
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.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→19.564 Å / Num. all: 77682 / Num. obs: 77682 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.16 Å2
Reflection shellResolution: 1.5→1.58 Å / % possible all: 97.1

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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: 1.502→19.564 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.862 / SU ML: 0.12 / σ(F): 1.99 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 3885 5 %Random
Rwork0.1994 73790 --
obs0.2006 77675 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.97 Å2 / Biso mean: 20.2861 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: LAST / Resolution: 1.502→19.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 83 260 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063093
X-RAY DIFFRACTIONf_angle_d1.164218
X-RAY DIFFRACTIONf_chiral_restr0.071494
X-RAY DIFFRACTIONf_plane_restr0.006549
X-RAY DIFFRACTIONf_dihedral_angle_d14.5421105
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 (%)
1.502-1.52030.23371360.23032570270699
1.5203-1.53960.26291380.227126242762100
1.5396-1.55980.26781370.217726082745100
1.5598-1.58120.27781360.216125892725100
1.5812-1.60370.24211360.212825772713100
1.6037-1.62770.23481380.20226282766100
1.6277-1.65310.23381370.200626032740100
1.6531-1.68020.26931370.210326022739100
1.6802-1.70910.24451380.204926202758100
1.7091-1.74020.24821380.203826122750100
1.7402-1.77360.2321370.201626122749100
1.7736-1.80980.23061370.206226082745100
1.8098-1.84910.22011380.210626132751100
1.8491-1.89210.24621380.21432616275499
1.8921-1.93940.21881370.205926122749100
1.9394-1.99180.27651380.205826272765100
1.9918-2.05030.26081410.202926732814100
2.0503-2.11640.22661370.198525992736100
2.1164-2.1920.23441400.204726562796100
2.192-2.27960.20711370.199826102747100
2.2796-2.38320.22131400.198826582798100
2.3832-2.50860.20221400.200726672807100
2.5086-2.66540.22161400.211226582798100
2.6654-2.87060.24361410.213726752816100
2.8706-3.15840.22561420.218926922834100
3.1584-3.6130.19211430.184827242867100
3.613-4.54260.20161440.16632740288499
4.5426-19.56560.20371440.18842717286193

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