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- PDB-2h8z: Xenobiotic Reductase A in complex with 8-Hydroxycoumarin -

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Basic information

Entry
Database: PDB / ID: 2h8z
TitleXenobiotic Reductase A in complex with 8-Hydroxycoumarin
ComponentsXenobiotic reductase A
KeywordsOXIDOREDUCTASE / beta-alpha barrel
Function / homology
Function and homology information


NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / NADP 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
8-HYDROXYCOUMARIN / FLAVIN MONONUCLEOTIDE / XenA
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.42 Å
AuthorsDobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Xenobiotic reductase A in the degradation of quinoline by Pseudomonas putida 86: physiological function, structure and mechanism of 8-hydroxycoumarin reduction.
Authors: Griese, J.J. / Jakob, R.P. / Schwarzinger, S. / Dobbek, H.
History
DepositionJun 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The strain is Pseudomonas putida 86 and not Pseudomonas putida KT2440 as in the aminoacid ...SEQUENCE The strain is Pseudomonas putida 86 and not Pseudomonas putida KT2440 as in the aminoacid sequence database reference

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xenobiotic reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20915
Polymers39,3051
Non-polymers1,90314
Water8,755486
1
A: Xenobiotic reductase A
hetero molecules

A: Xenobiotic reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,41730
Polymers78,6112
Non-polymers3,80728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)57.430, 83.340, 156.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Xenobiotic reductase A


Mass: 39305.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA / Production host: Escherichia coli (E. coli) / References: UniProt: Q88NF7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-8CM / 8-HYDROXYCOUMARIN / 8-HYDROXY-2H-CHROMENE-2-ONE


Mass: 162.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulphate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 23, 2005
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.42→20 Å / Num. all: 71212 / Num. obs: 67580 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.42→1.5 Å / % possible all: 85.5

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2H8X

2h8x


Resolution: 1.42→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.202 3379 Random
Rwork0.189 --
all0.192 71212 -
obs0.192 67580 -
Refinement stepCycle: LAST / Resolution: 1.42→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 117 486 3381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_bond_d0.0083
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3fmn_new.par
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5BTD_xplor.par

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