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- PDB-8pxk: Structure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved a... -

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Basic information

Entry
Database: PDB / ID: 8pxk
TitleStructure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 5.76 A
ComponentsFerredoxin reductase
KeywordsOXIDOREDUCTASE / BPHA4
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. KKS102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.77 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Senda, M. / Matsugaki, N. / Kawano, Y. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0072
Polymers43,2211
Non-polymers7861
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.186, 98.186, 170.292
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


Mass: 43221.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. KKS102 (bacteria) / Gene: bphA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52437
#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
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium formate Acetate buffer, pH 4.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 5.767 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 5.767 Å / Relative weight: 1
ReflectionResolution: 3.77→85.03 Å / Num. obs: 4614 / % possible obs: 86.62 % / Redundancy: 11.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1448 / Rpim(I) all: 0.04015 / Rrim(I) all: 0.1507 / Net I/σ(I): 21.38
Reflection shellResolution: 3.77→3.905 Å / Num. unique obs: 373 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 3.77→85.03 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.866 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.64 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19074 228 4.9 %RANDOM
Rwork0.18535 ---
obs0.18562 4387 86.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.146 Å2
Baniso -1Baniso -2Baniso -3
1--4.13 Å2-2.07 Å2-0 Å2
2---4.13 Å2-0 Å2
3---13.41 Å2
Refinement stepCycle: 1 / Resolution: 3.77→85.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 53 0 3058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163013
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.6454255
X-RAY DIFFRACTIONr_angle_other_deg0.4641.5666886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.375534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46910475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3983.5781611
X-RAY DIFFRACTIONr_mcbond_other2.3933.5791611
X-RAY DIFFRACTIONr_mcangle_it4.0316.4532012
X-RAY DIFFRACTIONr_mcangle_other4.0356.4542013
X-RAY DIFFRACTIONr_scbond_it6.6924.0811504
X-RAY DIFFRACTIONr_scbond_other6.214.0151501
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.6477.3722244
X-RAY DIFFRACTIONr_long_range_B_refined20.55244.313196
X-RAY DIFFRACTIONr_long_range_B_other20.55244.313197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.77→3.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 18 -
Rwork0.216 247 -
obs--72.4 %

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