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- PDB-5n2i: F420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound -

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Basic information

Entry
Database: PDB / ID: 5n2i
TitleF420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound
ComponentsReduced coenzyme F420:NADP oxidoreductase
KeywordsOXIDOREDUCTASE / F420:NADPH oxidoreductase / NADP+ bound / dimer of dimers
Function / homology
Function and homology information


coenzyme F420 binding / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / NADPH regeneration / oxidoreductase activity, acting on NAD(P)H / NADP binding
Similarity search - Function
NADPH-dependent F420 reductase / : / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Reduced coenzyme F420:NADP oxidoreductase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, H. / Nguyen, Q.-T. / Binda, C. / Mattevi, A. / Fraaije, M.W.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
European CommissionErasmus Mundus Action 2 project for Lot11 - Svaagata.eu Netherlands
University of GroningenUbbo Emius scholarship Netherlands
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Isolation and characterization of a thermostable F420:NADPH oxidoreductase from Thermobifida fusca.
Authors: Kumar, H. / Nguyen, Q.T. / Binda, C. / Mattevi, A. / Fraaije, M.W.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Database references / Category: citation / diffrn_radiation_wavelength
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reduced coenzyme F420:NADP oxidoreductase
B: Reduced coenzyme F420:NADP oxidoreductase
C: Reduced coenzyme F420:NADP oxidoreductase
D: Reduced coenzyme F420:NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,95015
Polymers97,3314
Non-polymers3,61811
Water10,809600
1
A: Reduced coenzyme F420:NADP oxidoreductase
B: Reduced coenzyme F420:NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6139
Polymers48,6662
Non-polymers1,9477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-15 kcal/mol
Surface area17140 Å2
MethodPISA
2
C: Reduced coenzyme F420:NADP oxidoreductase
D: Reduced coenzyme F420:NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3376
Polymers48,6662
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-16 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.389, 86.089, 136.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Reduced coenzyme F420:NADP oxidoreductase


Mass: 24332.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The residues that are not present in the coordinates have no clear electron density. They are thus disordered and not included in the final model.
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_0970 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47RA9, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3000, PEG400, glycerol, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9726 Å / Relative weight: 1
ReflectionResolution: 1.8→72.87 Å / Num. obs: 89383 / % possible obs: 98.6 % / Redundancy: 4.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 0.9 / Num. unique all: 4183 / CC1/2: 0.247 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAX

1jax


Resolution: 1.8→72.86 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.626 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21364 4458 5 %RANDOM
Rwork0.16458 ---
obs0.16703 84848 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.193 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--1.4 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.8→72.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6573 0 234 600 7407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196936
X-RAY DIFFRACTIONr_bond_other_d0.0030.026635
X-RAY DIFFRACTIONr_angle_refined_deg2.0162.0059448
X-RAY DIFFRACTIONr_angle_other_deg1.099315221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80822.917288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.237151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5491572
X-RAY DIFFRACTIONr_chiral_restr0.120.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217808
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021413
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_it2.3582.5293583
X-RAY DIFFRACTIONr_mcbond_other2.3512.5283582
X-RAY DIFFRACTIONr_mcangle_it3.2513.7814477
X-RAY DIFFRACTIONr_mcangle_other3.2533.7814478
X-RAY DIFFRACTIONr_scbond_it3.9233.0183353
X-RAY DIFFRACTIONr_scbond_other3.923.0183353
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9514.3464972
X-RAY DIFFRACTIONr_long_range_B_refined7.47132.2127478
X-RAY DIFFRACTIONr_long_range_B_other7.47132.2187479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 304 -
Rwork0.341 5666 -
obs--90.39 %

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