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- PDB-5cpl: The crystal structure of Xenobiotic reductase A (XenA) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 5cpl
TitleThe crystal structure of Xenobiotic reductase A (XenA) from Pseudomonas putida in complex with a nicotinamide mimic (mNH2)
ComponentsXenobiotic reductase
KeywordsOXIDOREDUCTASE / Reductase / Nicotinamide mimic / biomimetic
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
1-benzyl-1,4,5,6-tetrahydropyridine-3-carboxamide / Chem-FNR / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsKnaus, T. / Paul, C.E. / Levy, C.W. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Marie Curie IEF327647 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K0017802/1 United Kingdom
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 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xenobiotic reductase
B: Xenobiotic reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3187
Polymers81,9282
Non-polymers1,3895
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-38 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.800, 83.820, 155.880
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-536 / 1-benzyl-1,4,5,6-tetrahydropyridine-3-carboxamide


Mass: 216.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O
#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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate buffer pH 6.5, 40% v/v PEG 300 (JCSG+ HT96 A10 Molecular Dimensions)
Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→47.02 Å / Num. all: 102314 / Num. obs: 102314 / % possible obs: 98 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.0679 / Net I/σ(I): 17.41
Reflection shellResolution: 1.57→1.626 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.91 / % possible all: 96

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Processing

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

2h90


Resolution: 1.57→47.02 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 14.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1599 4868 4.92 %Random selection
Rwork0.1354 ---
obs0.1366 98960 94.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 95 797 6444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115892
X-RAY DIFFRACTIONf_angle_d1.2918042
X-RAY DIFFRACTIONf_dihedral_angle_d13.9892104
X-RAY DIFFRACTIONf_chiral_restr0.052840
X-RAY DIFFRACTIONf_plane_restr0.0071057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.58780.21841360.20782712X-RAY DIFFRACTION82
1.5878-1.60650.20561450.18392836X-RAY DIFFRACTION86
1.6065-1.62610.20551550.17792881X-RAY DIFFRACTION88
1.6261-1.64670.20421470.16452860X-RAY DIFFRACTION88
1.6467-1.66840.18131510.15962947X-RAY DIFFRACTION89
1.6684-1.69120.20341550.15422916X-RAY DIFFRACTION90
1.6912-1.71540.1961590.1492966X-RAY DIFFRACTION90
1.7154-1.7410.1691470.15122985X-RAY DIFFRACTION91
1.741-1.76820.19731620.15343010X-RAY DIFFRACTION92
1.7682-1.79720.20781480.14373016X-RAY DIFFRACTION93
1.7972-1.82820.16441590.14263100X-RAY DIFFRACTION93
1.8282-1.86140.17651740.13073093X-RAY DIFFRACTION94
1.8614-1.89720.15571800.13153092X-RAY DIFFRACTION95
1.8972-1.9360.16691650.12783143X-RAY DIFFRACTION96
1.936-1.97810.17031980.13023105X-RAY DIFFRACTION96
1.9781-2.02410.15471660.12883232X-RAY DIFFRACTION97
2.0241-2.07470.16341870.1253129X-RAY DIFFRACTION97
2.0747-2.13080.1381420.11983239X-RAY DIFFRACTION97
2.1308-2.19350.16731610.123224X-RAY DIFFRACTION97
2.1935-2.26430.14441820.11923225X-RAY DIFFRACTION97
2.2643-2.34520.16631610.11233225X-RAY DIFFRACTION98
2.3452-2.43910.16341610.11723294X-RAY DIFFRACTION98
2.4391-2.55010.13441450.11983274X-RAY DIFFRACTION98
2.5501-2.68460.15411730.11943306X-RAY DIFFRACTION99
2.6846-2.85280.15361600.12943297X-RAY DIFFRACTION99
2.8528-3.0730.16691630.14273322X-RAY DIFFRACTION99
3.073-3.38220.15211670.13763338X-RAY DIFFRACTION99
3.3822-3.87150.14321760.1313362X-RAY DIFFRACTION99
3.8715-4.87720.12341500.12473440X-RAY DIFFRACTION99
4.8772-53.39830.17771930.1723523X-RAY DIFFRACTION99

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