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- PDB-6pyz: Crystal Structure of human Tryptophan 2,3-dioxygenase in complex ... -

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Basic information

Entry
Database: PDB / ID: 6pyz
TitleCrystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in Active Site
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Tryptophan Dioxygenase / PF-06840003 / Oxidoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


response to nitroglycerin / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...response to nitroglycerin / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
Chem-H7S / PROTOPORPHYRIN IX CONTAINING FE / alpha-methyl-L-tryptophan / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPham, K.N. / Lewis-Ballester, A. / Yeh, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115773 United States
National Science Foundation (NSF, United States)CHE-1404929 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase.
Authors: Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)184,99816
Polymers180,7304
Non-polymers4,26812
Water19,3481074
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26700 Å2
ΔGint-173 kcal/mol
Surface area53580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.648, 154.158, 87.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-H7S / (3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione


Mass: 232.210 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H9FN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZIQ / alpha-methyl-L-tryptophan


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1074 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 50 mM Sodium Citrate (pH 5.6), 2% Tacsimate (pH 5.0) 5% PEG 3350
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.02→29.86 Å / Num. obs: 127544 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 1 / Net I/σ(I): 11.3
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 18361 / CC1/2: 0.39 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TI9

5ti9


Resolution: 2.02→29.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.978 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 6380 5 %RANDOM
Rwork0.1893 ---
obs0.1919 121109 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.76 Å2 / Biso mean: 50.459 Å2 / Biso min: 26.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0 Å2-0 Å2
2---0.14 Å20 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2.02→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11593 0 304 1074 12971
Biso mean--52.26 59.48 -
Num. residues----1376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01312208
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711247
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.67416506
X-RAY DIFFRACTIONr_angle_other_deg1.2871.59226001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50151367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04321.77729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.958152237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7391595
X-RAY DIFFRACTIONr_chiral_restr0.0660.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213482
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022819
LS refinement shellResolution: 2.02→2.072 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.369 501 -
Rwork0.35 8747 -
obs--98.82 %

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