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- PDB-4h4x: Crystal Structure of Ferredoxin reductase, BphA4 E175A/T176R/Q177... -

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Basic information

Entry
Database: PDB / ID: 4h4x
TitleCrystal Structure of Ferredoxin reductase, BphA4 E175A/T176R/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: 1.5 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 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 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)44,39411
Polymers43,1481
Non-polymers1,24610
Water5,621312
1
A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules

A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,78822
Polymers86,2962
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)98.215, 98.215, 170.804
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: 43148.164 Da / Num. of mol.: 1 / Mutation: E175A, 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.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 55.37 %
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: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: S1 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.5→19.58 Å / Num. all: 76902 / Num. obs: 76902 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.33 Å2
Reflection shellResolution: 1.5→1.58 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
MAR345300data 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→19.58 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.8718 / SU ML: 0.12 / σ(F): 1.99 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 3846 5 %Random
Rwork0.1907 73052 --
obs0.192 76898 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.9 Å2 / Biso mean: 18.9694 Å2 / Biso min: 7.75 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 83 312 3339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063095
X-RAY DIFFRACTIONf_angle_d1.194221
X-RAY DIFFRACTIONf_chiral_restr0.073492
X-RAY DIFFRACTIONf_plane_restr0.006551
X-RAY DIFFRACTIONf_dihedral_angle_d13.9831108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5190.20911390.21132622276197
1.519-1.5390.21181380.2032629276797
1.539-1.560.24511380.19332622276097
1.56-1.58230.20831380.19692621275997
1.5823-1.60590.21371390.19042651279097
1.6059-1.6310.21231390.18922625276497
1.631-1.65770.20021390.19512641278098
1.6577-1.68630.23941390.19042659279898
1.6863-1.7170.25271400.19772644278498
1.717-1.750.20541390.19332657279698
1.75-1.78570.23851420.19612689283198
1.7857-1.82450.2381400.19362654279498
1.8245-1.86690.25361400.20082667280798
1.8669-1.91350.20311420.19692693283598
1.9135-1.96520.24821410.19662686282798
1.9652-2.0230.22421420.19632687282999
2.023-2.08820.20571420.18652705284799
2.0882-2.16270.20251420.19012701284399
2.1627-2.24920.22311430.18542724286799
2.2492-2.35140.22181440.19092732287699
2.3514-2.47520.22071440.19772738288299
2.4752-2.62990.20891460.20462760290699
2.6299-2.83240.24121450.208627662911100
2.8324-3.11640.23631470.21272782292999
3.1164-3.5650.21891480.185628252973100
3.565-4.48260.20031520.167328793031100
4.4826-19.58160.1881580.17792993315199

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