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

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Basic information

Entry
Database: PDB / ID: 8pxl
TitleStructure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 1.37 A
ComponentsFerredoxin reductase
KeywordsOXIDOREDUCTASE / BPHA4
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, 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 / FORMIC ACID / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas sp. KKS102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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)44,3298
Polymers43,2211
Non-polymers1,1087
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-9 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.243, 98.243, 170.476
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


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.: 301 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.23 %
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: 1.378 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: 1.378 Å / Relative weight: 1
ReflectionResolution: 1.6→85.08 Å / Num. obs: 63940 / % possible obs: 98.9 % / Redundancy: 18 % / CC1/2: 1 / Rmerge(I) obs: 0.06567 / Rpim(I) all: 0.01556 / Rrim(I) all: 0.06753 / Net I/σ(I): 23.51
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 6081 / CC1/2: 0.467 / % possible all: 95.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→85.08 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.815 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20377 3150 4.9 %RANDOM
Rwork0.17741 ---
obs0.17865 60796 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.3 Å20 Å2
2---0.59 Å2-0 Å2
3---1.92 Å2
Refinement stepCycle: 1 / Resolution: 1.6→85.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 74 301 3380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123180
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163096
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.6564345
X-RAY DIFFRACTIONr_angle_other_deg0.4031.5747082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.599536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47110491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
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_it1.6532.6211627
X-RAY DIFFRACTIONr_mcbond_other1.6532.6221628
X-RAY DIFFRACTIONr_mcangle_it2.5064.7082036
X-RAY DIFFRACTIONr_mcangle_other2.5054.712037
X-RAY DIFFRACTIONr_scbond_it2.5582.9391553
X-RAY DIFFRACTIONr_scbond_other2.5582.9331544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.055.232302
X-RAY DIFFRACTIONr_long_range_B_refined6.00126.883520
X-RAY DIFFRACTIONr_long_range_B_other5.93626.093442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 239 -
Rwork0.306 4272 -
obs--95.77 %
Refinement TLS params.Method: refined / Origin x: 1.3664 Å / Origin y: 35.3512 Å / Origin z: 13.9506 Å
111213212223313233
T0.0493 Å20.0295 Å2-0.008 Å2-0.0492 Å20.0012 Å2--0.0051 Å2
L0.4814 °20.0613 °20.1837 °2-0.3794 °20.1625 °2--0.4256 °2
S0.032 Å °-0.007 Å °-0.0044 Å °-0.0655 Å °-0.0473 Å °0.0177 Å °0.005 Å °-0.0569 Å °0.0153 Å °

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