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- PDB-9b17: Crystal Structure of human Tryptophan 2,3-dioxygenase in complex ... -

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Basic information

Entry
Database: PDB / ID: 9b17
TitleCrystal Structure of human Tryptophan 2,3-dioxygenase in complex with PAN1 inhibitor
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE/INHIBITOR / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
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 / alpha-methyl-L-tryptophan / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGeeraerts, Z. / 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 Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151419 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase.
Authors: Geeraerts, Z. / Ishigami, I. / Lewis-Ballester, A. / Pham, K.N. / Kozlova, A. / Mathieu, C. / Frederick, R. / Yeh, S.R.
History
DepositionMar 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 11, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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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)185,45516
Polymers180,7304
Non-polymers4,72512
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25550 Å2
ΔGint-175 kcal/mol
Surface area55180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.61, 154.014, 88.58
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111HISHIS39 - 39123 - 375
211HISHIS39 - 39123 - 375
322PHEPHE39 - 38823 - 372
422PHEPHE39 - 38823 - 372
533LEULEU39 - 38923 - 373
633LEULEU39 - 38923 - 373
744PHEPHE39 - 38823 - 372
844PHEPHE39 - 38823 - 372
955LEULEU39 - 38923 - 373
1055LEULEU39 - 38923 - 373
1166PHEPHE39 - 38823 - 372
1266PHEPHE39 - 38823 - 372

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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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 BL21(DE3) (bacteria) / 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-A1AH9 / (5P)-5-(1H-indol-3-yl)-1-[2-(piperazin-1-yl)ethyl]-1H-1,2,3-benzotriazole


Mass: 346.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N6 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 50 mM Sodium Citrate pH 5.6, 2.0% Tacsimate pH 5.0, 5.0% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.648→34.29 Å / Num. obs: 36145 / % possible obs: 92.7 % / Redundancy: 4.83 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.998 / CC1/2 anomalous: -0.058 / Rmerge(I) obs: 0.1074 / Rpim(I) all: 0.0541 / Rrim(I) all: 0.1207 / AbsDiff over sigma anomalous: 0.795 / Baniso tensor eigenvalue 1: 53.5 Å2 / Baniso tensor eigenvalue 2: 87.8 Å2 / Baniso tensor eigenvalue 3: 111.2 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.647 Å / Aniso diffraction limit 2: 3.153 Å / Aniso diffraction limit 3: 3.348 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 10.89 / Num. measured all: 174706 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.5 / % possible ellipsoidal: 92.7 / % possible ellipsoidal anomalous: 91.5 / % possible spherical: 62.4 / % possible spherical anomalous: 60.6 / Redundancy anomalous: 2.57 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
8.511-34.294.690.02934.3384778477180718070.999-0.1590.01450.03260.68196.69696.69696.62.6796
6.733-8.5114.510.040925.7881608160180818080.998-0.1080.02140.04630.78396.897.996.897.996.82.4897.9
5.875-6.7334.330.063718.4478267826180618060.996-0.1130.0340.07250.79295.798.795.798.795.72.3798.7
5.331-5.8754.710.072517.3185208520180718070.995-0.0460.03680.08170.81697.198.597.198.597.12.5398.5
4.941-5.3314.860.074317.5387928792180818080.996-0.1110.03730.08340.79197.898.797.898.797.82.5998.7
4.647-4.9414.910.076517.1288788878180718070.9960.0260.0380.08570.83197.899.197.899.197.82.6299.1
4.413-4.6474.990.084315.5790169016180718070.996-00.04170.09440.80697.899.497.899.497.82.6699.4
4.217-4.4135.030.103113.8290849084180718070.994-0.0290.05110.11550.83498.299.798.299.798.22.6799.7
4.054-4.2175.060.126511.4591429142180818080.9930.0030.06190.14130.82897.899.797.899.797.82.6999.7
3.914-4.0545.070.16449.3191719171180818080.9840.0060.080.18340.80697.999.597.999.597.92.6999.5
3.79-3.9144.720.21317.2185138513180518050.97-0.0410.10890.24010.80398.699.498.699.498.62.4799.4
3.679-3.794.670.25276.0784448444180918090.968-0.0250.13050.28540.79798.399.598.399.598.32.4599.5
3.581-3.6794.830.30635.2187198719180618060.953-0.020.15450.34420.80598.399.998.399.998.32.5499.9
3.494-3.5814.750.40324.0685958595180818080.921-0.0070.20480.45390.7998.399.298.399.298.32.599.2
3.41-3.4944.490.48923.2781068106180718070.874-0.0240.25920.55580.79495.69795.69795.62.3597
3.328-3.414.830.58972.887418741180818080.855-0.0310.29920.66350.76986.18786.186.885.92.5387
3.244-3.3285.040.76822.2591079107180618060.775-0.0420.38020.85980.77486.78886.77978.52.6388
3.154-3.2445.160.78862.2193239323180818080.7690.0160.38570.88020.8178787.58765.665.32.6887.5
3.006-3.1544.910.77662.1488798879180718070.7580.0030.39170.87180.78771.371.471.334.534.22.5571.4
2.648-3.0065.10.87881.8492139213180818080.6110.0020.43220.98140.78661.962.261.9109.52.762.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROC1.0.5 20211020data reduction
STARANISO2.3.79data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→34.29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 37.231 / SU ML: 0.318 / Cross valid method: FREE R-VALUE / ESU R Free: 0.436
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2344 1788 4.948 %
Rwork0.1899 34349 -
all0.192 --
obs-36137 62.493 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.776 Å2
Baniso -1Baniso -2Baniso -3
1-1.588 Å2-0 Å20 Å2
2---0.576 Å2-0 Å2
3----1.013 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11616 0 340 19 11975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01212280
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611591
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.88916593
X-RAY DIFFRACTIONr_angle_other_deg0.4891.7926571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96251359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.056.111108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.342102251
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.47310647
X-RAY DIFFRACTIONr_chiral_restr0.0630.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214427
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023125
X-RAY DIFFRACTIONr_nbd_refined0.2420.22861
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.211052
X-RAY DIFFRACTIONr_nbtor_refined0.1960.26075
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.26386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.218
X-RAY DIFFRACTIONr_nbd_other0.1970.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.23
X-RAY DIFFRACTIONr_mcbond_it3.0883.7145474
X-RAY DIFFRACTIONr_mcbond_other3.0813.7135472
X-RAY DIFFRACTIONr_mcangle_it5.1616.6596819
X-RAY DIFFRACTIONr_mcangle_other5.166.6596819
X-RAY DIFFRACTIONr_scbond_it3.4154.0666806
X-RAY DIFFRACTIONr_scbond_other3.4144.0656805
X-RAY DIFFRACTIONr_scangle_it5.7977.349774
X-RAY DIFFRACTIONr_scangle_other5.7977.349775
X-RAY DIFFRACTIONr_lrange_it10.51445.01552411
X-RAY DIFFRACTIONr_lrange_other10.51445.01552408
X-RAY DIFFRACTIONr_ncsr_local_group_10.1090.0511884
X-RAY DIFFRACTIONr_ncsr_local_group_20.1140.0511361
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.0511674
X-RAY DIFFRACTIONr_ncsr_local_group_40.1190.0511373
X-RAY DIFFRACTIONr_ncsr_local_group_50.1180.0511693
X-RAY DIFFRACTIONr_ncsr_local_group_60.1170.0511404
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.109270.05009
12AX-RAY DIFFRACTIONLocal ncs0.109270.05009
23AX-RAY DIFFRACTIONLocal ncs0.113730.05009
24AX-RAY DIFFRACTIONLocal ncs0.113730.05009
35AX-RAY DIFFRACTIONLocal ncs0.112980.05009
36AX-RAY DIFFRACTIONLocal ncs0.112980.05009
47AX-RAY DIFFRACTIONLocal ncs0.118550.05009
48AX-RAY DIFFRACTIONLocal ncs0.118550.05009
59AX-RAY DIFFRACTIONLocal ncs0.117520.05009
510AX-RAY DIFFRACTIONLocal ncs0.117520.05009
611AX-RAY DIFFRACTIONLocal ncs0.117390.05009
612AX-RAY DIFFRACTIONLocal ncs0.117390.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.7180.29160.28172X-RAY DIFFRACTION4.2472
2.718-2.7920.331130.338270X-RAY DIFFRACTION6.9295
2.792-2.8730.245180.31384X-RAY DIFFRACTION10.1056
2.873-2.9610.44230.33535X-RAY DIFFRACTION14.3114
2.961-3.0570.35380.276799X-RAY DIFFRACTION22.2843
3.057-3.1630.333690.2791460X-RAY DIFFRACTION42.1096
3.163-3.2820.3321240.2732322X-RAY DIFFRACTION69.6668
3.282-3.4140.2721280.2592760X-RAY DIFFRACTION85.1917
3.414-3.5650.2671690.2343009X-RAY DIFFRACTION98.0562
3.565-3.7370.251340.2072964X-RAY DIFFRACTION99.8067
3.737-3.9360.2291530.1882820X-RAY DIFFRACTION99.498
3.936-4.1710.211580.1612651X-RAY DIFFRACTION99.6099
4.171-4.4550.1781410.1412519X-RAY DIFFRACTION99.5137
4.455-4.8050.2291020.1372378X-RAY DIFFRACTION99.5185
4.805-5.2530.1781190.1452152X-RAY DIFFRACTION98.7391
5.253-5.8560.221050.1761972X-RAY DIFFRACTION98.5294
5.856-6.7290.242870.2041767X-RAY DIFFRACTION98.617
6.729-8.1630.257880.1841485X-RAY DIFFRACTION97.7019
8.163-11.2310.161580.1611201X-RAY DIFFRACTION97.2201
11.231-34.290.294550.234730X-RAY DIFFRACTION95.0363
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8323-1.5188-0.66944.02120.41290.7643-0.0089-0.0194-0.1116-0.3048-0.01230.454-0.0962-0.23560.02120.06030.0563-0.0450.12040.00980.1571-39.342337.0769-0.9675
24.0968-0.325-2.08360.84410.32671.7598-0.2678-0.271-0.47590.00190.0744-0.1630.13880.41190.19340.06940.0152-0.05560.12560.02180.2673-5.46116.697-10.7638
31.94940.56630.60943.29151.87712.41060.06820.6446-0.072-0.6459-0.28230.9687-0.1271-0.63070.21410.30280.1005-0.21430.5839-0.00950.4048-28.168133.0154-28.5531
42.0091-0.1085-0.23981.62130.08623.59160.0004-0.52870.23130.22450.0628-0.2631-0.00650.323-0.06320.03320.0107-0.0420.2108-0.04660.186-7.075542.58934.2375
Refinement TLS groupSelection: ALL

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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