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- PDB-5tia: Crystal structure of human TDO in complex with Trp, Northeast Str... -

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Basic information

Entry
Database: PDB / ID: 5tia
TitleCrystal structure of human TDO in complex with Trp, Northeast Structural Genomics Consortium Target HR6161
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / human tryptophan 2 / 3-dioxygenase
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 / TRYPTOPHAN / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.441 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)184,83016
Polymers180,7304
Non-polymers4,10012
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26590 Å2
ΔGint-183 kcal/mol
Surface area51880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.359, 153.561, 88.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
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 13, 2014 / Details: vertical focusing mirror
RadiationMonochromator: Bent single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 73126 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.086 / Net I/av σ(I): 31.2 / Net I/σ(I): 32
Reflection shellResolution: 2.44→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.6 / % possible all: 63.4

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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: 5TI9

5ti9


Resolution: 2.441→35.133 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.21
RfactorNum. reflection% reflection
Rfree0.2298 7362 10.1 %
Rwork0.168 --
obs0.1743 72907 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.441→35.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11295 0 292 474 12061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811883
X-RAY DIFFRACTIONf_angle_d1.07716050
X-RAY DIFFRACTIONf_dihedral_angle_d17.1024429
X-RAY DIFFRACTIONf_chiral_restr0.0421656
X-RAY DIFFRACTIONf_plane_restr0.0052021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.441-2.46880.34272090.24771758X-RAY DIFFRACTION82
2.4688-2.49780.34492530.23682168X-RAY DIFFRACTION100
2.4978-2.52830.30412430.22142193X-RAY DIFFRACTION100
2.5283-2.56030.27722210.20012187X-RAY DIFFRACTION100
2.5603-2.59390.29092420.19282192X-RAY DIFFRACTION100
2.5939-2.62950.25042350.18872153X-RAY DIFFRACTION100
2.6295-2.6670.27292550.20462174X-RAY DIFFRACTION100
2.667-2.70680.27032630.20682138X-RAY DIFFRACTION100
2.7068-2.74910.26782570.19452209X-RAY DIFFRACTION100
2.7491-2.79410.27842460.19572150X-RAY DIFFRACTION100
2.7941-2.84230.29382390.20382195X-RAY DIFFRACTION100
2.8423-2.8940.26592430.18742202X-RAY DIFFRACTION100
2.894-2.94960.2542210.19542201X-RAY DIFFRACTION100
2.9496-3.00980.26632520.1982180X-RAY DIFFRACTION100
3.0098-3.07520.27272670.20172165X-RAY DIFFRACTION100
3.0752-3.14670.28942380.19612184X-RAY DIFFRACTION100
3.1467-3.22530.26952260.1932190X-RAY DIFFRACTION100
3.2253-3.31250.27312640.19312191X-RAY DIFFRACTION100
3.3125-3.40980.22682540.17862193X-RAY DIFFRACTION100
3.4098-3.51980.21542280.16632218X-RAY DIFFRACTION100
3.5198-3.64550.21982450.15792191X-RAY DIFFRACTION100
3.6455-3.79130.22292490.15062195X-RAY DIFFRACTION100
3.7913-3.96360.19332440.15382204X-RAY DIFFRACTION100
3.9636-4.17230.21272450.13782235X-RAY DIFFRACTION100
4.1723-4.43320.18232280.1252238X-RAY DIFFRACTION100
4.4332-4.77470.16932730.12662199X-RAY DIFFRACTION100
4.7747-5.25380.1882720.13292207X-RAY DIFFRACTION100
5.2538-6.01070.2552460.16752270X-RAY DIFFRACTION100
6.0107-7.56050.20922560.17082273X-RAY DIFFRACTION100
7.5605-35.13620.20932480.17352292X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 20.11 Å / Origin y: -45.0447 Å / Origin z: -35.3192 Å
111213212223313233
T0.202 Å2-0.0054 Å2-0.0122 Å2-0.1961 Å2-0.0059 Å2--0.2003 Å2
L0.6722 °20.2616 °2-0.3111 °2-0.5709 °2-0.2744 °2--0.5325 °2
S-0.0007 Å °-0.0224 Å °-0.0404 Å °0.0162 Å °-0.0298 Å °-0.0173 Å °-0.0249 Å °0.0328 Å °-0.0008 Å °
Refinement TLS groupSelection details: all

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