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- PDB-2gr2: Crystal structure of Ferredoxin reductase, BphA4 (oxidized form) -

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Basic information

Entry
Database: PDB / ID: 2gr2
TitleCrystal structure of Ferredoxin reductase, BphA4 (oxidized form)
Componentsferredoxin reductase
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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-DIPHOSPHORIBOSE / FLAVIN-ADENINE DINUCLEOTIDE / : / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. KKS102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.85 Å
AuthorsSenda, T. / Senda, M.
CitationJournal: To be Published
Title: A ferredoxin reductase BphA4 uses a butterfly motion of FAD to regulate affinity for ferredoxin
Authors: Senda, M. / Kishigami, S. / Kimura, S. / Ishida, T. / Fukuda, M. / Senda, T.
History
DepositionApr 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: 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)44,5663
Polymers43,2211
Non-polymers1,3452
Water4,197233
1
A: ferredoxin reductase
hetero molecules

A: ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1326
Polymers86,4422
Non-polymers2,6904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)98.683, 98.683, 172.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe second part of the biological assembly is generated by (x, x-y, 1/6-z).

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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-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
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: 1.85→50 Å / Num. all: 42769 / Num. obs: 42769 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 22
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.7 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
XTALVIEWrefinement
RefinementMethod to determine structure: Difference Fourier / Resolution: 1.85→32.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.483 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23742 2129 5 %RANDOM
Rwork0.19898 ---
all0.20089 40127 --
obs0.20089 40127 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.3 Å20 Å2
2---0.59 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 89 233 3299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223151
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5692.0094312
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91322.56125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11115466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3331533
X-RAY DIFFRACTIONr_chiral_restr0.1070.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022391
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21400
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22157
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8881.52072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29823211
X-RAY DIFFRACTIONr_scbond_it2.27231238
X-RAY DIFFRACTIONr_scangle_it3.534.51097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 140 -
Rwork0.237 2712 -
obs--90.28 %
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)
10.9084-0.42670.22881.41270.54420.8621-0.0394-0.07750.00520.1022-0.02680.13360.0468-0.06490.0662-0.09290.00140.0245-0.1372-0.0187-0.083353.8212.17712.036
20.80470.2167-0.130.8266-0.31831.0621-0.09580.1452-0.0422-0.00480.0309-0.1628-0.08740.24910.0649-0.0851-0.05180.0009-0.0011-0.0085-0.047181.34720.7764.931
32.6097-0.3953-0.24142.73441.86764.3452-0.215-0.38240.13570.60290.0739-0.15740.2280.14650.14110.06780.0378-0.0713-0.0748-0.0189-0.071674.91919.5432.765
42.07711.33510.75031.971.62191.4391-0.0374-0.0974-0.1283-0.01790.14650.019-0.1139-0.084-0.10920.14150.01210.00270.0948-0.01760.157363.3712.9079.452
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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