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- PDB-7p46: Crystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxyg... -

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Basic information

Entry
Database: PDB / ID: 7p46
TitleCrystal Structure of Xanthomonas campestris Tryptophan 2,3-dioxygenase (TDO)
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / cyanide / kynurenine
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 / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / TRYPTOPHAN / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKwon, H. / Basran, J. / Booth, E.S. / Campbell, L.P. / Thackray, S.J. / Moody, P.C.E. / Mowat, C.G. / Raven, E.L.
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Binding of l-kynurenine to X. campestris tryptophan 2,3-dioxygenase.
Authors: Basran, J. / Booth, E.S. / Campbell, L.P. / Thackray, S.J. / Jesani, M.H. / Clayden, J. / Moody, P.C.E. / Mowat, C.G. / Kwon, H. / Raven, E.L.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Tryptophan 2,3-dioxygenase
F: Tryptophan 2,3-dioxygenase
G: Tryptophan 2,3-dioxygenase
H: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,21552
Polymers263,5398
Non-polymers9,67744
Water34,6611924
1
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)136,91030
Polymers131,7694
Non-polymers5,14126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35330 Å2
ΔGint-244 kcal/mol
Surface area35430 Å2
MethodPISA
2
E: Tryptophan 2,3-dioxygenase
F: Tryptophan 2,3-dioxygenase
G: Tryptophan 2,3-dioxygenase
H: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,30522
Polymers131,7694
Non-polymers4,53618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34190 Å2
ΔGint-232 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.095, 117.752, 138.819
Angle α, β, γ (deg.)90.000, 95.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Tryptophan 2,3-dioxygenase / TDO / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / Tryptophan pyrrolase / Tryptophanase


Mass: 32942.332 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: kynA, XCC0432 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PDA8, tryptophan 2,3-dioxygenase

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Non-polymers , 6 types, 1968 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CN
#4: Chemical
ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H12N2O3
#5: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H12N2O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1924 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 1000, MES (2-(N-morpholino)ethanesulfonic acid) pH 6.3, bicine (N,N-bis(2-hydroxyethyl)glycine) pH 9.0, MnCl2, MgCl2, sodium cyanide and L-Trp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97828 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97828 Å / Relative weight: 1
ReflectionResolution: 1.7→117 Å / Num. obs: 268120 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 2.9 / Num. unique obs: 34391

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NW8

2nw8


Resolution: 1.7→89.78 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.117 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 13541 5.1 %RANDOM
Rwork0.1488 ---
obs0.1507 254545 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.54 Å2 / Biso mean: 23.854 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.7→89.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18397 0 680 1924 21001
Biso mean--25.15 37.09 -
Num. residues----2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01320242
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718350
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.67627674
X-RAY DIFFRACTIONr_angle_other_deg1.4841.58842322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24852410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.79720.9241256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.277153335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.53115201
X-RAY DIFFRACTIONr_chiral_restr0.0970.22404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0223160
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024915
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 839 -
Rwork0.274 15517 -
all-16356 -
obs--81.23 %

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