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- PDB-5cpm: XenA from Pseudomonas putida in complex with NADPH4. -

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Basic information

Entry
Database: PDB / ID: 5cpm
TitleXenA from Pseudomonas putida in complex with NADPH4.
ComponentsXenobiotic reductase
KeywordsOXIDOREDUCTASE / XenA
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-FNR / Chem-NDP / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKnaus, T. / Paul, C.E. / Levy, C.W. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes.
Authors: Knaus, T. / Paul, C.E. / Levy, C.W. / de Vries, S. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jan 10, 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: Xenobiotic reductase
B: Xenobiotic reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3366
Polymers81,9282
Non-polymers2,4084
Water17,312961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-39 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.368, 83.991, 157.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Xenobiotic reductase / Xenobiotic reductase A


Mass: 40964.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R9V9
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NADPH4 complex was grown from 0.06 M (magnesium chloride, calcium chloride), 0.1 M (Tris (base), Bicine) buffer system pH 8.5, 30 % v/v GOL P4K (60% v/v Glycerol: PEG 4K) (Morpheus HT96 A11 Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.5→74.16 Å / Num. obs: 122500 / % possible obs: 99 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.48
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.251 / Mean I/σ(I) obs: 1.92 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXdev_1977refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H90

2h90


Resolution: 1.5→74.16 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 5987 4.9 %Random
Rwork0.1539 ---
obs0.1559 122152 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→74.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 128 961 6641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065940
X-RAY DIFFRACTIONf_angle_d1.0278132
X-RAY DIFFRACTIONf_dihedral_angle_d12.6122102
X-RAY DIFFRACTIONf_chiral_restr0.044859
X-RAY DIFFRACTIONf_plane_restr0.0051064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.3371980.26383799X-RAY DIFFRACTION98
1.517-1.53490.28881840.25133751X-RAY DIFFRACTION99
1.5349-1.55360.3372080.24223851X-RAY DIFFRACTION99
1.5536-1.57330.28012000.23693753X-RAY DIFFRACTION99
1.5733-1.5940.30251930.22413819X-RAY DIFFRACTION99
1.594-1.61580.30541840.22153840X-RAY DIFFRACTION99
1.6158-1.63890.2791930.20813828X-RAY DIFFRACTION99
1.6389-1.66340.25361730.18843812X-RAY DIFFRACTION99
1.6634-1.68940.26952150.18353822X-RAY DIFFRACTION99
1.6894-1.71710.23042070.18413790X-RAY DIFFRACTION99
1.7171-1.74670.25832130.18553850X-RAY DIFFRACTION99
1.7467-1.77840.25011750.18093829X-RAY DIFFRACTION99
1.7784-1.81270.27492010.16423858X-RAY DIFFRACTION99
1.8127-1.84970.19292040.15863864X-RAY DIFFRACTION99
1.8497-1.88990.19251770.14453818X-RAY DIFFRACTION100
1.8899-1.93380.19932090.1413872X-RAY DIFFRACTION100
1.9338-1.98220.20791810.14423881X-RAY DIFFRACTION100
1.9822-2.03580.19732010.14153881X-RAY DIFFRACTION100
2.0358-2.09570.19662050.14063834X-RAY DIFFRACTION100
2.0957-2.16340.18022050.12963899X-RAY DIFFRACTION100
2.1634-2.24070.17211910.12763869X-RAY DIFFRACTION100
2.2407-2.33040.16761960.12873904X-RAY DIFFRACTION100
2.3304-2.43650.18022140.13443896X-RAY DIFFRACTION100
2.4365-2.56490.18592170.13463880X-RAY DIFFRACTION100
2.5649-2.72560.13841900.13133963X-RAY DIFFRACTION100
2.7256-2.93610.16651940.14193915X-RAY DIFFRACTION100
2.9361-3.23160.17322280.14713935X-RAY DIFFRACTION100
3.2316-3.69920.15742050.13673956X-RAY DIFFRACTION100
3.6992-4.66050.13392140.12814007X-RAY DIFFRACTION100
4.6605-74.25340.1762120.16084189X-RAY DIFFRACTION100

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