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- PDB-4h4w: Crystal Structure of Ferredoxin reductase, BphA4 E175C/T176R/Q177... -

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Basic information

Entry
Database: PDB / ID: 4h4w
TitleCrystal Structure of Ferredoxin reductase, BphA4 E175C/T176R/Q177G mutant (reduced 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Biphenyl dioxygenase ferredoxin reductase subunit
Similarity search - Component
Biological speciesAcidovorax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)44,9398
Polymers43,1801
Non-polymers1,7597
Water4,143230
1
A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules

A: Biphenyl dioxygenase ferredoxin reductase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,87916
Polymers86,3602
Non-polymers3,51814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)98.023, 98.023, 171.088
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 230 / 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: 55.23 %
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: S1 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→84.89 Å / Num. all: 53954 / Num. obs: 53954 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.88 Å2
Reflection shellResolution: 1.7→1.79 Å / % possible all: 99.6

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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: 2YVF

2yvf


Resolution: 1.7→47.116 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8532 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2696 5 %Random
Rwork0.1988 51255 --
obs0.1997 53951 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.4 Å2 / Biso mean: 25.5302 Å2 / Biso min: 9.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 108 230 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073108
X-RAY DIFFRACTIONf_angle_d1.2034262
X-RAY DIFFRACTIONf_chiral_restr0.072502
X-RAY DIFFRACTIONf_plane_restr0.005550
X-RAY DIFFRACTIONf_dihedral_angle_d15.4281106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.73090.23221380.216726202758100
1.7309-1.76420.26011380.226326492787100
1.7642-1.80030.24051380.231726402778100
1.8003-1.83940.27241400.226626542794100
1.8394-1.88220.2371400.221226582798100
1.8822-1.92930.25121390.215626522791100
1.9293-1.98140.24481400.202626402780100
1.9814-2.03970.25471400.204926712811100
2.0397-2.10560.2461400.206526502790100
2.1056-2.18080.24511420.205927032845100
2.1808-2.26810.22181410.205726772818100
2.2681-2.37140.24421410.205626712812100
2.3714-2.49640.21571420.211627002842100
2.4964-2.65280.22141430.215227222865100
2.6528-2.85760.23891430.223326992842100
2.8576-3.14510.23831440.21827342878100
3.1451-3.60.17781450.189827572902100
3.6-4.53510.1781460.163727922938100
4.5351-47.13440.18951560.17792966312299

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