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- PDB-3e08: H55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 300000000
TitleH55S mutant Xanthomonas campestris tryptophan 2,3-dioxygenase
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / TDO / heme / tryptophan 2 / 3-dioxygenase / H55S / Dioxygenase
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
PROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMowat, C.G. / Campbell, L.P.
CitationJournal: Biochemistry / Year: 2008
Title: Histidine 55 of tryptophan 2,3-dioxygenase is not an active site base but regulates catalysis by controlling substrate binding
Authors: Thackray, S.J. / Bruckmann, C. / Anderson, J.L. / Campbell, L.P. / Xiao, R. / Zhao, L. / Mowat, C.G. / Forouhar, F. / Tong, L. / Chapman, S.K.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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

Downloads & links

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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)285,07332
Polymers276,8748
Non-polymers8,19924
Water35,2191955
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)142,53716
Polymers138,4374
Non-polymers4,10012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31910 Å2
ΔGint-244.6 kcal/mol
Surface area36280 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)142,53716
Polymers138,4374
Non-polymers4,10012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31500 Å2
ΔGint-240 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.912, 117.718, 138.978
Angle α, β, γ (deg.)90.00, 95.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tryptophan 2,3-dioxygenase /


Mass: 34609.215 Da / Num. of mol.: 8 / Mutation: H55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: xccb100_0466 / Plasmid: pMGK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8PDA8, tryptophan 2,3-dioxygenase
#2: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1955 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 9-10% PEG1000, 80mM MES (pH6.3), 20mM bicine (pH9.0), 40mM MnCl2, 400mM MgCl2, 8-15mM NaCN, 20mM L-Trp, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.045 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 1.9→17.56 Å / Num. obs: 189203 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 23.24 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / Num. unique all: 24898 / % possible all: 87.1

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Processing

Software
NameClassification
PHENIXrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NW7

2nw7


Resolution: 1.9→17.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 18212 5.03 %random
Rwork0.1776 ---
all-362159 --
obs-189203 93.63 %-
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18341 0 584 1955 20880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d0.952
X-RAY DIFFRACTIONf_bond_d0.007
LS refinement shellResolution: 1.9→1.9216 Å
RfactorNum. reflection% reflection
Rfree0.2881 524 -
Rwork0.2624 --
obs-9911 0.82 %

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