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- PDB-5zbc: Crystal structure of Se-Met tryptophan oxidase (C395A mutant) fro... -

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Basic information

Entry
Database: PDB / ID: 5zbc
TitleCrystal structure of Se-Met tryptophan oxidase (C395A mutant) from Chromobacterium violaceum
ComponentsFlavin-dependent L-tryptophan oxidase VioA
KeywordsOXIDOREDUCTASE / Oxidase
Function / homology
Function and homology information


7-chloro-L-tryptophan oxidase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsYamaguchi, H. / Tatsumi, M. / Takahashi, K. / Tagami, U. / Sugiki, M. / Kashiwagi, T. / Okazaki, S. / Mizukoshi, T. / Asano, Y.
CitationJournal: J. Biochem. / Year: 2018
Title: Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis.
Authors: Yamaguchi, H. / Tatsumi, M. / Takahashi, K. / Tagami, U. / Sugiki, M. / Kashiwagi, T. / Kameya, M. / Okazaki, S. / Mizukoshi, T. / Asano, Y.
History
DepositionFeb 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-dependent L-tryptophan oxidase VioA
B: Flavin-dependent L-tryptophan oxidase VioA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6534
Polymers102,0822
Non-polymers1,5712
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-21 kcal/mol
Surface area33660 Å2
Unit cell
Length a, b, c (Å)87.980, 89.080, 113.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flavin-dependent L-tryptophan oxidase VioA / Tryptophan Oxidase


Mass: 51040.914 Da / Num. of mol.: 2 / Mutation: C395A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: vioA, CV_3274 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M MES, 40% Polyethylene glycol 400, pH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→70.07 Å / Num. obs: 45946 / % possible obs: 100 % / Redundancy: 14.595 % / Biso Wilson estimate: 38.053 Å2 / Rmerge F obs: 0.042 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.079 / Net I/σ(I): 21.09 / Num. measured all: 670570 / Scaling rejects: 804
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.314.8150.1130.2949.3883292562256220.305100
2.3-2.414.8150.0980.2411.1270800477947790.249100
2.4-2.514.8130.080.19413.2259562402140210.201100
2.5-2.714.7930.0740.15615.7794643639863980.161100
2.7-314.7160.0590.11719.8798522669566950.121100
3-414.6440.0260.06228.9615388210508105080.064100
4-514.3740.0180.05334.4554505379237920.054100
5-1013.7720.0190.0634.4749372358535850.062100
10-70.0710.9740.0260.07131.8859925645460.07596.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
SOLVEphasing
RefinementResolution: 2.2→70.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2361 / WRfactor Rwork: 0.1784 / FOM work R set: 0.863 / SU B: 5.099 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2495 / SU Rfree: 0.2007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 2319 5 %RANDOM
Rwork0.1713 ---
obs0.1741 43626 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.02 Å2 / Biso mean: 34.804 Å2 / Biso min: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0 Å2
2--2.26 Å2-0 Å2
3----1.69 Å2
Refinement stepCycle: final / Resolution: 2.2→70.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 106 348 6844
Biso mean--23.7 40.24 -
Num. residues----818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196676
X-RAY DIFFRACTIONr_bond_other_d0.0010.026176
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9759043
X-RAY DIFFRACTIONr_angle_other_deg0.848314166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84222.772303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7021549
X-RAY DIFFRACTIONr_chiral_restr0.1020.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021645
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 151 -
Rwork0.182 3186 -
all-3337 -
obs--100 %

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