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- PDB-2gr0: Crystal structure of Ferredoxin reductase, BphA4 (oxidized form, ... -

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Basic information

Entry
Database: PDB / ID: 2gr0
TitleCrystal structure of Ferredoxin reductase, BphA4 (oxidized form, NAD+ complex)
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
ADENOSINE-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / : / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. KKS102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.7 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 3, 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)44,4343
Polymers43,2211
Non-polymers1,2132
Water5,441302
1
A: ferredoxin reductase
hetero molecules

A: ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8686
Polymers86,4422
Non-polymers2,4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)98.283, 98.283, 171.245
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2M Sodium formate, 0.1M Sodium acetate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 53813 / Num. obs: 53813 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.6 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: Difference Fourier / Resolution: 1.7→32.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.273 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20854 2732 5.1 %RANDOM
Rwork0.19233 ---
all0.19317 51060 --
obs0.19317 51060 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.061 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.51 Å20 Å2
2---1.02 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 80 302 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3852.0024284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.38522.5128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41315474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1361534
X-RAY DIFFRACTIONr_chiral_restr0.090.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022382
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21462
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22140
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.781.52047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16223184
X-RAY DIFFRACTIONr_scbond_it1.92131235
X-RAY DIFFRACTIONr_scangle_it3.0914.51099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 191 -
Rwork0.224 3465 -
obs--93.77 %
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)
10.7622-0.36320.1881.03960.3720.6384-0.0388-0.05460.01740.07680.00510.05650.0297-0.04560.0337-0.00960.00860.0137-0.0492-0.0124-0.041553.74312.13811.937
20.45280.1843-0.15860.7361-0.31210.9343-0.05090.0913-0.0349-0.00810.0045-0.1028-0.0770.18490.0465-0.0446-0.03930.00710.0109-0.0161-0.042281.18520.694.881
32.1729-0.5114-0.28262.32331.64163.7322-0.1881-0.3030.11270.4740.0628-0.12120.17720.1270.12530.06690.0362-0.0515-0.045-0.0186-0.078374.77919.5732.839
40.56550.72170.34261.16120.60390.3233-0.0870.18090.0215-0.05340.08310.004-0.06730.16570.00390.02950.0180.00010.0055-0.022-0.00963.23912.9019.365
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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