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- PDB-5ti9: Crystal structure of human TDO in complex with Trp and dioxygen, ... -

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Basic information

Entry
Database: PDB / ID: 5ti9
TitleCrystal structure of human TDO in complex with Trp and dioxygen, Northeast Structural Genomics Consortium Target HR6161
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Human Tryptophan 2 / 3-dioxygenase in complex with Trp and O2
Function / homology
Function and homology information


response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / N'-Formylkynurenine / OXYGEN MOLECULE / PHOSPHATE ION / TRYPTOPHAN / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsForouhar, F. / Lewis-Ballester, A. / Lew, S. / Karkashon, S. / Seetharaman, J. / Yeh, S.R. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 GM62413 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM074958 United States
CitationJournal: Sci Rep / Year: 2016
Title: Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase.
Authors: Lewis-Ballester, A. / Forouhar, F. / Kim, S.M. / Lew, S. / Wang, Y. / Karkashon, S. / Seetharaman, J. / Batabyal, D. / Chiang, B.Y. / Hussain, M. / Correia, M.A. / Yeh, S.R. / Tong, L.
History
DepositionOct 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Structure summary
Revision 1.3Nov 30, 2016Group: Structure summary
Revision 1.4Dec 14, 2016Group: Structure summary
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 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 / struct_conn
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
Revision 1.8Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,14820
Polymers180,7304
Non-polymers4,41816
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26770 Å2
ΔGint-194 kcal/mol
Surface area52830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.601, 154.009, 87.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 45182.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDO2, TDO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P48775, tryptophan 2,3-dioxygenase

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Non-polymers , 6 types, 452 molecules

#2: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NFK / N'-Formylkynurenine / (2S)-2-amino-4-[2-(formylamino)phenyl]-4-oxobutanoic acid


Mass: 236.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.6
Details: 50 mM sodium citrate (pH 5.6), 5% (w/v) PEG 3350 and 2% (w/v) Tacsimate (pH 5)
PH range: 5.6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 14, 2014 / Details: vertical focusing mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 68351 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.041 / Net I/av σ(I): 35.2 / Net I/σ(I): 37.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 4.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NW8

2nw8


Resolution: 2.5→33.932 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.23 6879 10.09 %
Rwork0.1586 --
obs0.1658 68151 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11324 0 310 436 12070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111926
X-RAY DIFFRACTIONf_angle_d1.28316095
X-RAY DIFFRACTIONf_dihedral_angle_d17.54469
X-RAY DIFFRACTIONf_chiral_restr0.051657
X-RAY DIFFRACTIONf_plane_restr0.0062030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4954-2.52370.31522240.23351911X-RAY DIFFRACTION95
2.5237-2.55340.30262310.20611991X-RAY DIFFRACTION100
2.5534-2.58460.25972280.19162065X-RAY DIFFRACTION100
2.5846-2.61730.29932370.18851994X-RAY DIFFRACTION100
2.6173-2.65170.26942190.18822033X-RAY DIFFRACTION100
2.6517-2.6880.25652500.18851995X-RAY DIFFRACTION100
2.688-2.72640.26452100.17742033X-RAY DIFFRACTION100
2.7264-2.76710.30512280.18642059X-RAY DIFFRACTION100
2.7671-2.81030.26142170.18642037X-RAY DIFFRACTION100
2.8103-2.85630.27882350.19352027X-RAY DIFFRACTION100
2.8563-2.90560.27732510.19141989X-RAY DIFFRACTION100
2.9056-2.95840.27022350.18132016X-RAY DIFFRACTION100
2.9584-3.01520.26412040.18352058X-RAY DIFFRACTION100
3.0152-3.07670.26212340.18252007X-RAY DIFFRACTION100
3.0767-3.14360.27272230.18242067X-RAY DIFFRACTION100
3.1436-3.21670.24872310.18582026X-RAY DIFFRACTION100
3.2167-3.2970.2612360.19452036X-RAY DIFFRACTION100
3.297-3.38610.27712130.18122052X-RAY DIFFRACTION100
3.3861-3.48560.23012170.17262047X-RAY DIFFRACTION100
3.4856-3.5980.21182240.15382050X-RAY DIFFRACTION100
3.598-3.72650.21342340.14352041X-RAY DIFFRACTION100
3.7265-3.87550.23742270.1442066X-RAY DIFFRACTION100
3.8755-4.05160.20612290.14282065X-RAY DIFFRACTION100
4.0516-4.26480.18512450.12762033X-RAY DIFFRACTION100
4.2648-4.53140.19392130.12192089X-RAY DIFFRACTION100
4.5314-4.88040.17242460.11982070X-RAY DIFFRACTION100
4.8804-5.36980.21352410.13492066X-RAY DIFFRACTION100
5.3698-6.14280.2442560.1582087X-RAY DIFFRACTION100
6.1428-7.72420.21752230.15482130X-RAY DIFFRACTION100
7.7242-33.93470.19522180.1582132X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 19.9988 Å / Origin y: -44.6925 Å / Origin z: -34.9832 Å
111213212223313233
T0.1587 Å2-0.0239 Å2-0.0139 Å2-0.1583 Å2-0.0067 Å2--0.1572 Å2
L0.5359 °20.2304 °2-0.2857 °2-0.5008 °2-0.2333 °2--0.5683 °2
S0.0155 Å °-0.0161 Å °-0.0637 Å °0.0511 Å °-0.0343 Å °-0.0514 Å °-0.0742 Å °0.0538 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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