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- PDB-2nw7: Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xantho... -

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Basic information

Entry
Database: PDB / ID: 2nw7
TitleCrystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferric heme. Northeast Structural Genomics Target XcR13
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / all alpha-helical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / L-tryptophan 2,3-dioxygenase activity / L-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 2,3-dioxygenase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsForouhar, F. / Anderson, J.L.R. / Mowat, C.G. / Hussain, A. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Tucker, T. / Ho, C.K. / Ma, L.C. ...Forouhar, F. / Anderson, J.L.R. / Mowat, C.G. / Hussain, A. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Tucker, T. / Ho, C.K. / Ma, L.C. / Cunningham, K. / Janjua, H. / Zhao, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Chapman, S.K. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase.
Authors: Forouhar, F. / Anderson, J.L. / Mowat, C.G. / Vorobiev, S.M. / Hussain, A. / Abashidze, M. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Tucker, T. / Xiao, R. / Ma, L.C. / Zhao, L. / ...Authors: Forouhar, F. / Anderson, J.L. / Mowat, C.G. / Vorobiev, S.M. / Hussain, A. / Abashidze, M. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Tucker, T. / Xiao, R. / Ma, L.C. / Zhao, L. / Acton, T.B. / Montelione, G.T. / Chapman, S.K. / Tong, L.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)145,3928
Polymers142,9264
Non-polymers2,4664
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23910 Å2
ΔGint-187 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.939, 109.359, 125.513
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: 35731.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: pv. campestris / Gene: XCC0432 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8PDA8
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 50mM MES, 12% PEG1000, 60mM Manganese chloride, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→46.43 Å / Num. all: 37833 / Num. obs: 37833 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.093 / Net I/σ(I): 10.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.74 / Rsym value: 0.268 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YW0

1yw0


Resolution: 2.7→46.43 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 60586.54 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: XtalView was also the program used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2491 10.1 %RANDOM
Rwork0.257 ---
obs0.257 24715 72 %-
all-32665 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.7119 Å2 / ksol: 0.322951 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.11 Å20 Å20 Å2
2---13.88 Å20 Å2
3---23.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8643 0 172 142 8957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 183 10.1 %
Rwork0.257 1623 -
obs--53.6 %

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