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- PDB-2yvf: Crystal structure of ferredoxin reductase BPHA4 (hydroquinone) -

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Basic information

Entry
Database: PDB / ID: 2yvf
TitleCrystal structure of ferredoxin reductase BPHA4 (hydroquinone)
ComponentsFerredoxin reductase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / flavin adenine dinucleotide 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 / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.6 Å
AuthorsSenda, T. / Senda, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin
Authors: Senda, M. / Kishigami, S. / Kimura, S. / Fukuda, M. / Ishida, T. / Senda, T.
History
DepositionApr 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9008
Polymers43,2211
Non-polymers1,6797
Water3,729207
1
A: Ferredoxin reductase
hetero molecules

A: Ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,80116
Polymers86,4422
Non-polymers3,35814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)97.597, 97.597, 169.463
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 Ferredoxin reductase / ferredoxin reductase BPHA4


Mass: 43221.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: strain KKS102 / Gene: bphA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52437, ferredoxin-NADP+ 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 5.40, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 60816 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.54
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 3.1 / % possible all: 94.4

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Processing

Software
NameVersionClassification
XTALVIEWrefinement
REFMAC5.2.0005refinement
ADSCdata collection
XDSdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.191 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3036 5 %RANDOM
Rwork0.188 ---
obs0.189 57683 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å20 Å2
2---0.36 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 112 207 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223150
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.422.0134303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69922.927123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3971530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022383
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21509
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22154
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.52051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16823200
X-RAY DIFFRACTIONr_scbond_it1.97831225
X-RAY DIFFRACTIONr_scangle_it3.1284.51100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 214 -
Rwork0.236 4065 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.915-0.34520.29591.15330.33120.8661-0.0638-0.11650.04850.09850.06140.01570.0104-0.07110.0023-0.00990.02270.0124-0.0714-0.0288-0.050853.723212.205711.8856
21.83890.34290.49771.1924-0.17691.5223-0.21680.40360.0919-0.00860.1102-0.1884-0.19850.42420.1066-0.0614-0.10550.00290.0613-0.0214-0.009980.781320.54145.2311
32.38920.0332-0.58962.9842.05365.773-0.068-0.35270.0610.51460.0327-0.16610.1690.1420.03530.03010.0566-0.0956-0.0764-0.0452-0.079574.731520.000132.9383
42.8291-0.25641.98141.22380.06351.726-0.11360.16280.08720.01660.179-0.0264-0.15470.1745-0.06530.02470.0233-0.0086-0.0223-0.0455-0.005863.427612.92349.4269
528.054112.21870.865617.7879-5.12212.4525-0.1247-0.6856-0.40480.65330.0687-0.8159-0.74370.19340.0560.1757-0.0285-0.00990.1214-0.0090.15571.753822.822810.5559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1116 - 111
2X-RAY DIFFRACTION1AA238 - 317238 - 317
3X-RAY DIFFRACTION2AA112 - 237112 - 237
4X-RAY DIFFRACTION3AA318 - 406318 - 406
5X-RAY DIFFRACTION4AB14491
6X-RAY DIFFRACTION5AC15001

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