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- PDB-2nw8: Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xantho... -

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Basic information

Entry
Database: PDB / ID: 2nw8
TitleCrystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferrous heme and tryptophan. 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


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: 1.6 Å
AuthorsForouhar, F. / Anderson, J.L.R. / Mowat, C.G. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / Ho, C.K. / Ma, L.C. / Cunningham, K. / Janjua, H. ...Forouhar, F. / Anderson, J.L.R. / Mowat, C.G. / Bruckmann, C. / Thackray, S.J. / Seetharaman, J. / 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. / Champman, 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 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,62310
Polymers71,4632
Non-polymers2,1608
Water12,755708
1
A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,24520
Polymers142,9264
Non-polymers4,32016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area25850 Å2
ΔGint-219 kcal/mol
Surface area36500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.093, 114.094, 96.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Tryptophan 2,3-dioxygenase /


Mass: 35731.422 Da / Num. of mol.: 2
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-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100mM MES, 10% PEG4000, 60mM Manganese chloride, 10mM Sodium dithionite, 2mM L-tryptophan, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2006 / 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: 1.6→24.54 Å / Num. all: 94048 / Num. obs: 94048 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.056 / Net I/σ(I): 23.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.93 / Rsym value: 0.5 / % possible all: 99

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Processing

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

1yw0


Resolution: 1.6→19.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 73316.13 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: XtalView was also the program used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4176 5.1 %RANDOM
Rwork0.171 ---
obs0.171 82660 86.6 %-
all-94048 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9792 Å2 / ksol: 0.36883 e/Å3
Displacement parametersBiso mean: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.5 Å20 Å2
2---0.11 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 148 708 5256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
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: 1.6→1.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.22 290 4.7 %
Rwork0.189 5836 -
obs--64.8 %

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