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- PDB-6ud5: Crystal structure of human tryptophan 2,3-dioxygenase in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ud5
TitleCrystal structure of human tryptophan 2,3-dioxygenase in complex with carbon monoxide and tryptophan
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Tryptophan Dioxygenase / carbon monoxide / Tryptophan
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: 2021
Title: Conformational Plasticity in Human Heme-Based Dioxygenases.
Authors: Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R.
History
DepositionSep 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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)184,94220
Polymers180,7304
Non-polymers4,21216
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27120 Å2
ΔGint-192 kcal/mol
Surface area54020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.725, 154.493, 88.306
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 / Fragment: UNP residues 18-389
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
#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5
Details: 50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350
PH range: 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 MX325HE / Detector: CCD / Date: Apr 8, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.05→19.97 Å / Num. obs: 120121 / % possible obs: 96.7 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 7.9
Reflection shellResolution: 2.05→2.16 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 16664 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TI9

5ti9


Resolution: 2.05→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.865 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 6206 5.2 %RANDOM
Rwork0.1828 ---
obs0.1846 113859 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.59 Å2 / Biso mean: 37.501 Å2 / Biso min: 20.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0 Å2-0 Å2
2---0.45 Å20 Å2
3---1.23 Å2
Refinement stepCycle: final / Resolution: 2.05→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11632 0 300 773 12705
Biso mean--31.99 42.07 -
Num. residues----1394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01312243
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711239
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.66616537
X-RAY DIFFRACTIONr_angle_other_deg1.1961.58925961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20951387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31921.685730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.645152215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7611595
X-RAY DIFFRACTIONr_chiral_restr0.0570.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213567
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022842
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 479 -
Rwork0.302 7861 -
all-8340 -
obs--92.22 %

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