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- PDB-5zbd: Crystal structure of tryptophan oxidase (C395A mutant) from Chrom... -

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Basic information

Entry
Database: PDB / ID: 5zbd
TitleCrystal structure of 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 / TRYPTOPHAN / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)102,9366
Polymers100,9562
Non-polymers1,9804
Water13,691760
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-21 kcal/mol
Surface area33810 Å2
Unit cell
Length a, b, c (Å)87.860, 89.270, 112.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 50478.180 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
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-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→69.98 Å / Num. obs: 82681 / % possible obs: 100 % / Redundancy: 7.325 % / Biso Wilson estimate: 26.033 Å2 / Rmerge F obs: 0.06 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.103 / Net I/σ(I): 14.45 / Num. measured all: 605654
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
1.8-1.97.3410.1760.2746.828990012246122460.295100
1.9-27.3530.1210.1959.2872943992099200.21100
2-2.17.3640.0920.15311.3159704811081080.164100
2.1-2.27.3690.0710.12613.0549808676067590.136100
2.2-2.37.3850.0630.11314.2341304559355930.121100
2.3-2.57.3880.0540.115.8664606874787450.108100
2.5-37.3690.0440.08818.129576812996129960.095100
3-47.3120.0370.08320.727638610447104460.089100
4-57.2030.0370.08321.8427092376137610.089100
5-69.986.8520.0390.08721.2128143412741070.09499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.368
Highest resolutionLowest resolution
Rotation47.65 Å3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XSCALEdata scaling
MOLREP11.2.05phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→69.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.304 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20225 4141 5 %RANDOM
Rwork0.15755 ---
obs0.15981 78540 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å20 Å2
2--0.16 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.8→69.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 136 760 7348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196780
X-RAY DIFFRACTIONr_bond_other_d0.0010.026263
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9659186
X-RAY DIFFRACTIONr_angle_other_deg0.9314389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22323.173312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.609151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9231545
X-RAY DIFFRACTIONr_chiral_restr0.120.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021649
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0241.9633302
X-RAY DIFFRACTIONr_mcbond_other2.0231.9633301
X-RAY DIFFRACTIONr_mcangle_it2.8892.9324117
X-RAY DIFFRACTIONr_mcangle_other2.8892.9324118
X-RAY DIFFRACTIONr_scbond_it3.0792.2963478
X-RAY DIFFRACTIONr_scbond_other3.0782.2963479
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7413.3055070
X-RAY DIFFRACTIONr_long_range_B_refined6.60417.5558668
X-RAY DIFFRACTIONr_long_range_B_other6.42917.0058336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 319 -
Rwork0.176 5736 -
obs--100 %

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