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- PDB-3l5l: Xenobiotic Reductase A - oxidized -

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Basic information

Entry
Database: PDB / ID: 3l5l
TitleXenobiotic Reductase A - oxidized
ComponentsXenobiotic reductase A
KeywordsOXIDOREDUCTASE / TIM barrel
Function / homology
Function and homology information


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
(R,R)-2,3-BUTANEDIOL / FLAVIN MONONUCLEOTIDE / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.03 Å
AuthorsSpiegelhauer, O. / Dobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Cysteine as a modulator residue in the active site of xenobiotic reductase A: a structural, thermodynamic and kinetic study
Authors: Spiegelhauer, O. / Mende, S. / Dickert, F. / Knauer, S.H. / Ullmann, G.M. / Dobbek, H.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: 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 / 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

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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)41,31312
Polymers39,9141
Non-polymers1,39911
Water10,485582
1
A: Xenobiotic reductase A
hetero molecules

A: Xenobiotic reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,62624
Polymers79,8282
Non-polymers2,79822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2720 Å2
ΔGint-17 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.893, 83.416, 156.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1673-

HOH

21A-1772-

HOH

31A-1935-

HOH

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Components

#1: Protein Xenobiotic reductase A


Mass: 39914.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: 86 / Gene: xenA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q3ZDM6*PLUS, NADPH dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PSEUDOMONAS PUTIDA STRAIN 86 DOES NOT CURRENTLY EXIST.

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Ammonium sulfate, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.02→30 Å / Num. all: 186337 / Num. obs: 180933 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.3 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2H8X

2h8x


Resolution: 1.03→29.341 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.921 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 13.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1477 9045 5 %random
Rwork0.1293 ---
all0.1302 180933 --
obs0.1302 180915 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.465 Å2 / ksol: 0.433 e/Å3
Displacement parametersBiso max: 73.63 Å2 / Biso mean: 15.345 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-2.053 Å2-0 Å2-0 Å2
2---0.727 Å20 Å2
3----1.326 Å2
Refinement stepCycle: LAST / Resolution: 1.03→29.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 84 582 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013126
X-RAY DIFFRACTIONf_angle_d1.4234308
X-RAY DIFFRACTIONf_dihedral_angle_d18.2931162
X-RAY DIFFRACTIONf_chiral_restr0.084459
X-RAY DIFFRACTIONf_plane_restr0.013561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.03-1.0670.2868120.27154241623688
1.067-1.110.2088750.203166281750395
1.11-1.160.1838890.162168901777996
1.16-1.2210.168980.141170621796097
1.221-1.2980.1439090.123172671817698
1.298-1.3980.149140.11173641827899
1.398-1.5390.1219230.095175431846699
1.539-1.7610.1089310.0891770018631100
1.761-2.2190.1229380.1051781418752100
2.219-29.3530.1489560.1311817819134100

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