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- PDB-1yw0: Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomo... -

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Basic information

Entry
Database: PDB / ID: 1yw0
TitleCrystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.
Componentstryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / tryptophan / dioxygenase / NESG / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / heme binding / metal ion binding
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / Tryptophan/Indoleamine 2,3-dioxygenase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Forouhar, F. / Kuzin, A. / Xiao, R. / Ciano, M. / Aton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.
Authors: Vorobiev, S.M. / Abashidze, M. / Forouhar, F. / Kuzin, A. / Xiao, R. / Ciano, M. / Aton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tryptophan 2,3-dioxygenase
B: tryptophan 2,3-dioxygenase
C: tryptophan 2,3-dioxygenase
D: tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,75412
Polymers129,5604
Non-polymers1948
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-170 kcal/mol
Surface area38310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.701, 110.223, 149.398
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
tryptophan 2,3-dioxygenase


Mass: 32389.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
Species: Xanthomonas campestris / Strain: pv. campestris str. ATCC 33913 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8PDA8, tryptophan 2,3-dioxygenase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13-20% PEG 3350, 0.1-0.2 M magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9686 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 71669 / Num. obs: 71669 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / % possible all: 82.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.32 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 123416.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2510 3.9 %RANDOM
Rwork0.25 ---
obs0.25 64280 81.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.7539 Å2 / ksol: 0.318839 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.02 Å20 Å20 Å2
2---5.67 Å20 Å2
3---9.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8165 0 8 105 8278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.992
X-RAY DIFFRACTIONc_scbond_it2.722
X-RAY DIFFRACTIONc_scangle_it4.022.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 394 4.4 %
Rwork0.321 8514 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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