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- PDB-3bk9: H55A mutant of tryptophan 2,3-dioxygenase from Xanthomonas campestris -

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Basic information

Entry
Database: PDB / ID: 3bk9
TitleH55A mutant of tryptophan 2,3-dioxygenase from Xanthomonas campestris
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / tryptophan dioxygenase / H55A mutant / heme
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: 2.15 Å
AuthorsBruckmann, C. / Mowat, C.G.
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.R. / Campbell, L.P. / Xiao, R. / Zhao, L. / Mowat, C.G. / Forouhar, F. / Tong, L. / Chapman, S.K.
History
DepositionDec 6, 2007Deposition 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_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)292,90229
Polymers285,3158
Non-polymers7,58721
Water18,3031016
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)146,75716
Polymers142,6574
Non-polymers4,10012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29920 Å2
ΔGint-227 kcal/mol
Surface area36050 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)146,14413
Polymers142,6574
Non-polymers3,4879
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24530 Å2
ΔGint-198 kcal/mol
Surface area35390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.222, 117.606, 139.283
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tryptophan 2,3-dioxygenase / TDO


Mass: 35664.355 Da / Num. of mol.: 8 / Mutation: H55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
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


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100mM Mes (pH 6.3), 10-12% (wt/vol) PEG 4000, 60mM MnCl2, 10mM sodium dithionite, 2mM L-Trp, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.381 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.381 Å / Relative weight: 1
ReflectionResolution: 2.15→59.66 Å / Num. all: 312593 / Num. obs: 131764 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.5 / Num. unique all: 18137 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2nw7

2nw7


Resolution: 2.15→54.13 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.864 / SU B: 7.708 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28457 6624 5 %RANDOM
Rwork0.20047 ---
obs0.2047 125104 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.189 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20.17 Å2
2---1.05 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.15→54.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17638 0 419 1016 19073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02218564
X-RAY DIFFRACTIONr_angle_refined_deg2.3462.00425273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55452109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94822.753977
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.023153042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.08815188
X-RAY DIFFRACTIONr_chiral_restr0.1710.22606
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214480
X-RAY DIFFRACTIONr_nbd_refined0.2270.28829
X-RAY DIFFRACTIONr_nbtor_refined0.3080.212272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3710.21025
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4430.28
X-RAY DIFFRACTIONr_mcbond_it1.3151.511067
X-RAY DIFFRACTIONr_mcangle_it1.994217053
X-RAY DIFFRACTIONr_scbond_it3.53138941
X-RAY DIFFRACTIONr_scangle_it5.0644.58208
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 455 -
Rwork0.265 8633 -
obs-8633 90.65 %

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