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- PDB-3l67: Xenobiotic reductase A - C25S variant -

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Basic information

Entry
Database: PDB / ID: 3l67
TitleXenobiotic reductase A - C25S variant
ComponentsXenobiotic reductase A
KeywordsOXIDOREDUCTASE / FMN / flavin / old-yellow-enzyme family
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: 1.8 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 23, 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)41,11710
Polymers39,8981
Non-polymers1,2199
Water9,620534
1
A: Xenobiotic reductase A
hetero molecules

A: Xenobiotic reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,23420
Polymers79,7962
Non-polymers2,43818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2740 Å2
ΔGint-17 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.991, 83.612, 157.240
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-427-

HOH

21A-431-

HOH

31A-442-

HOH

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Components

#1: Protein Xenobiotic reductase A


Mass: 39897.953 Da / Num. of mol.: 1 / Mutation: C25S
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.: 1 / 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.: 534 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PSEUDOMONAS PUTIDA STRAIN 86 DOES NOT CURRENTLY ...A SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PSEUDOMONAS PUTIDA STRAIN 86 DOES NOT CURRENTLY EXIST. THIS PROTEIN IS C25S MUTANT.

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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: 48.51 %
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: 0.92 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→33.15 Å / Num. all: 68504 / Num. obs: 64188 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3L5L

3l5l


Resolution: 1.8→33.15 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.846 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 3211 5 %Random
Rwork0.1821 ---
all0.1845 64188 --
obs0.1845 64185 93.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.169 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 55.51 Å2 / Biso mean: 17.894 Å2 / Biso min: 5.17 Å2
Baniso -1Baniso -2Baniso -3
1-9.084 Å2-0 Å2-0 Å2
2---5.583 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 72 534 3378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062917
X-RAY DIFFRACTIONf_angle_d0.9643984
X-RAY DIFFRACTIONf_dihedral_angle_d17.9481011
X-RAY DIFFRACTIONf_chiral_restr0.064419
X-RAY DIFFRACTIONf_plane_restr0.009514
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 (%)
1.8-1.8640.3592740.3045294556881
1.864-1.9390.2873010.2295588588986
1.939-2.0270.3023100.2095857616790
2.027-2.1340.2623330.1966290662397
2.134-2.2680.243390.1836444678399
2.268-2.4430.2513410.1876395673698
2.443-2.6880.2353340.186324665897
2.688-3.0770.2493240.1776294661897
3.077-3.8760.1963220.1576225654796
3.876-33.1560.1693330.1556263659696

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