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- PDB-2gqw: Crystal structure of Ferredoxin reductase, BphA4 (oxidized form) -

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Basic information

Entry
Database: PDB / ID: 2gqw
TitleCrystal structure of Ferredoxin reductase, BphA4 (oxidized form)
Componentsferredoxin reductase
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / 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 / : / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. KKS102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.4 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 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 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)44,3298
Polymers43,2211
Non-polymers1,1087
Water7,927440
1
A: ferredoxin reductase
hetero molecules

A: ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,65816
Polymers86,4422
Non-polymers2,21614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)98.409, 98.409, 170.582
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. KKS102 (bacteria) / Production host: Escherichia coli (E. coli)
References: GenBank: 9929802, UniProt: Q52437*PLUS, ferredoxin-NADP+ 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.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 55.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 2M Sodium formate, 0.1M Sodium acetate, pH 5.3, 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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. all: 1342357 / Num. obs: 1342357 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.8
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 14 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 5.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
XDSdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: Difference Fourier / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.567 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4814 5 %RANDOM
Rwork0.17793 ---
all0.17882 91184 --
obs0.17882 91184 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 74 440 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9974284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3295412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18522.619126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3315469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3851533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21461
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22154
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2342
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7661.52070
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17323226
X-RAY DIFFRACTIONr_scbond_it1.89331194
X-RAY DIFFRACTIONr_scangle_it2.8714.51052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 358 -
Rwork0.209 6573 -
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)
10.5416-0.2510.16180.80350.28820.5247-0.0207-0.05120.00540.04510.00630.04620.0268-0.04880.0144-0.01060.00920.0117-0.0451-0.0063-0.023253.855412.220511.9323
20.38410.2303-0.23770.5746-0.2990.5114-0.02760.0602-0.03740.0060.007-0.0781-0.07560.15260.0206-0.0134-0.03610.01190.0094-0.0126-0.019481.33420.72424.9465
31.6371-0.0951-0.04872.05361.27142.722-0.106-0.2630.08450.3552-0.0351-0.02110.05740.03220.14110.0540.0128-0.0311-0.0216-0.0147-0.04874.800219.54632.7453
41.84550.60711.33060.59340.58411.0138-0.08960.03830.01140.00330.05760.0237-0.10660.06860.03210.01090.01090.0078-0.0285-0.0117-0.007963.411512.95099.3267
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

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