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- PDB-7a62: Structure of human indoleamine-2,3-dioxygenase 1 (hIDO1) with a c... -

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Basic information

Entry
Database: PDB / ID: 7a62
TitleStructure of human indoleamine-2,3-dioxygenase 1 (hIDO1) with a complete JK loop
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / dioxygenase / tryptophan catabolism / heme-binding / enzyme
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / : / quinolinate biosynthetic process ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / : / quinolinate biosynthetic process / positive regulation of type 2 immune response / stereocilium bundle / L-tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of interleukin-10 production / T cell proliferation / multicellular organismal response to stress / negative regulation of T cell proliferation / swimming behavior / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase signature 1. / Indoleamine 2,3-dioxygenase signature 2. / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43796448682 Å
AuthorsMirgaux, M. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Not funded Belgium
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1.
Authors: Mirgaux, M. / Leherte, L. / Wouters, J.
History
DepositionAug 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
SupersessionDec 30, 2020ID: 6TUE
Revision 1.1Mar 10, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Mar 17, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.id
Revision 1.3Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Indoleamine 2,3-dioxygenase 1
B: Indoleamine 2,3-dioxygenase 1
C: Indoleamine 2,3-dioxygenase 1
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,38517
Polymers181,2044
Non-polymers3,18213
Water12,520695
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0093
Polymers45,3011
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1024
Polymers45,3011
Non-polymers8013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1375
Polymers45,3011
Non-polymers8364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1375
Polymers45,3011
Non-polymers8364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.960, 117.950, 216.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-791-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILE(chain A and (resseq 12:14 or (resid 15 and (name...AA12 - 4214 - 44
12HISHISPROPRO(chain A and (resseq 12:14 or (resid 15 and (name...AA45 - 10447 - 106
13ASNASNTYRTYR(chain A and (resseq 12:14 or (resid 15 and (name...AA106 - 145108 - 147
14ASNASNLEULEU(chain A and (resseq 12:14 or (resid 15 and (name...AA147 - 197149 - 199
15ALAALALEULEU(chain A and (resseq 12:14 or (resid 15 and (name...AA199 - 207201 - 209
16ALAALAPROPRO(chain A and (resseq 12:14 or (resid 15 and (name...AA210 - 223212 - 225
17ALAALAARGARG(chain A and (resseq 12:14 or (resid 15 and (name...AA225 - 296227 - 298
18TYRTYRARGARG(chain A and (resseq 12:14 or (resid 15 and (name...AA298 - 317300 - 319
19PHEPHEGLNGLN(chain A and (resseq 12:14 or (resid 15 and (name...AA319 - 361321 - 363
110GLYGLYLEULEU(chain A and (resseq 12:14 or (resid 15 and (name...AA380 - 400382 - 402
211SERSERILEILE(chain B and (resseq 12:14 or (resid 15 and (name...BB12 - 4214 - 44
212HISHISPROPRO(chain B and (resseq 12:14 or (resid 15 and (name...BB45 - 10447 - 106
213ASNASNTYRTYR(chain B and (resseq 12:14 or (resid 15 and (name...BB106 - 145108 - 147
214ASNASNLEULEU(chain B and (resseq 12:14 or (resid 15 and (name...BB147 - 197149 - 199
215ALAALALEULEU(chain B and (resseq 12:14 or (resid 15 and (name...BB199 - 207201 - 209
216ALAALAPROPRO(chain B and (resseq 12:14 or (resid 15 and (name...BB210 - 223212 - 225
217ALAALAARGARG(chain B and (resseq 12:14 or (resid 15 and (name...BB225 - 296227 - 298
218TYRTYRARGARG(chain B and (resseq 12:14 or (resid 15 and (name...BB298 - 317300 - 319
219PHEPHEGLNGLN(chain B and (resseq 12:14 or (resid 15 and (name...BB319 - 361321 - 363
220GLYGLYLEULEU(chain B and (resseq 12:14 or (resid 15 and (name...BB380 - 400382 - 402
321SERSERILEILE(chain C and (resseq 12:14 or (resid 15 and (name...CC12 - 4214 - 44
322HISHISPROPRO(chain C and (resseq 12:14 or (resid 15 and (name...CC45 - 10447 - 106
323ASNASNTYRTYR(chain C and (resseq 12:14 or (resid 15 and (name...CC106 - 145108 - 147
324ASNASNLEULEU(chain C and (resseq 12:14 or (resid 15 and (name...CC147 - 197149 - 199
325ALAALALEULEU(chain C and (resseq 12:14 or (resid 15 and (name...CC199 - 207201 - 209
326ALAALAPROPRO(chain C and (resseq 12:14 or (resid 15 and (name...CC210 - 223212 - 225
327ALAALAARGARG(chain C and (resseq 12:14 or (resid 15 and (name...CC225 - 296227 - 298
328TYRTYRARGARG(chain C and (resseq 12:14 or (resid 15 and (name...CC298 - 317300 - 319
329PHEPHEGLNGLN(chain C and (resseq 12:14 or (resid 15 and (name...CC319 - 361321 - 363
330GLYGLYLEULEU(chain C and (resseq 12:14 or (resid 15 and (name...CC380 - 400382 - 402
431SERSERILEILE(chain D and (resseq 12:14 or (resid 15 and (name...DD12 - 4214 - 44
432HISHISPROPRO(chain D and (resseq 12:14 or (resid 15 and (name...DD45 - 10447 - 106
433ASNASNTYRTYR(chain D and (resseq 12:14 or (resid 15 and (name...DD106 - 145108 - 147
434ASNASNLEULEU(chain D and (resseq 12:14 or (resid 15 and (name...DD147 - 197149 - 199
435ALAALALEULEU(chain D and (resseq 12:14 or (resid 15 and (name...DD199 - 207201 - 209
436ALAALAPROPRO(chain D and (resseq 12:14 or (resid 15 and (name...DD210 - 223212 - 225
437ALAALAARGARG(chain D and (resseq 12:14 or (resid 15 and (name...DD225 - 296227 - 298
438TYRTYRARGARG(chain D and (resseq 12:14 or (resid 15 and (name...DD298 - 317300 - 319
439PHEPHEGLNGLN(chain D and (resseq 12:14 or (resid 15 and (name...DD319 - 361321 - 363
440GLYGLYLEULEU(chain D and (resseq 12:14 or (resid 15 and (name...DD380 - 400382 - 402

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Components

#1: Protein
Indoleamine 2,3-dioxygenase 1 / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 45300.898 Da / Num. of mol.: 4 / Mutation: K116A, K117A
Source method: isolated from a genetically manipulated source
Details: Gol and HEM are ligands. / Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.83 Å3/Da / Density % sol: 56.6 % / Description: red, rectangular, plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 14% IN PEG 3350, 0.1 M IN PHOSPHATE BUFFER AT A PH OF 6.25 PROTEIN : IN HEPES 5 MM AND NACL 200MM CRYOPROTECTION IN 20% OF GLYCEROL AND 20 MM OF SODIUM DITHIONITE, PH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2019
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.438→49.18 Å / Num. obs: 77982 / % possible obs: 84 % / Redundancy: 13 % / Biso Wilson estimate: 38.98 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1677 / Rrim(I) all: 0.1742 / Net I/σ(I): 8.81
Reflection shellResolution: 2.438→2.525 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.828 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 4879 / CC1/2: 0.753 / CC star: 0.927 / Rrim(I) all: 1.907 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Cootmodel building
XDSdata reduction
PHASERphasing
MxCuBEdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+43 / Resolution: 2.43796448682→49.1760318032 Å / SU ML: 0.323919810868 / Cross valid method: FREE R-VALUE / σ(F): 0.00224499941129 / Phase error: 32.9741722185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257286553269 3301 5.02251841032 %
Rwork0.211611041463 62423 -
obs0.214105983061 65724 84.115953158 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.8337568823 Å2
Refinement stepCycle: LAST / Resolution: 2.43796448682→49.1760318032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12178 0 0 695 12873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013615428275712475
X-RAY DIFFRACTIONf_angle_d1.0477783230816935
X-RAY DIFFRACTIONf_chiral_restr0.06022841132321831
X-RAY DIFFRACTIONf_plane_restr0.007137261669492159
X-RAY DIFFRACTIONf_dihedral_angle_d15.8207952277406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.438-2.47280.4513557160161080.3975154651651825X-RAY DIFFRACTION60.1244167963
2.4728-2.50970.4342162995941010.3601417563312007X-RAY DIFFRACTION65.6493304267
2.5097-2.54890.4180781331521160.3333069862252002X-RAY DIFFRACTION66.2496090084
2.5489-2.59070.3303922162951130.3312760572862092X-RAY DIFFRACTION68.6060983199
2.5907-2.63540.4144595793741090.3077333895282183X-RAY DIFFRACTION71.3796325132
2.6354-2.68330.2943957055291250.2734977231592226X-RAY DIFFRACTION72.7413366337
2.6833-2.73490.3555825785711190.2657307290932290X-RAY DIFFRACTION75.046728972
2.7349-2.79070.3292206449841220.2662480368792387X-RAY DIFFRACTION78.0161691542
2.7907-2.85140.3409792258721220.2758493882282407X-RAY DIFFRACTION78.4186046512
2.8514-2.91770.3205882202881330.2727548480012451X-RAY DIFFRACTION80.6743677802
2.9177-2.99070.2752994696741400.2661221498882572X-RAY DIFFRACTION83.6004932182
2.9907-3.07150.3415087183971360.2554302750652601X-RAY DIFFRACTION85.132192846
3.0715-3.16190.3183337664531350.2528050259932674X-RAY DIFFRACTION86.5372766482
3.1619-3.26390.2960875408541420.2414608536682709X-RAY DIFFRACTION88.0753784368
3.2639-3.38050.2895824710581500.2447681178482786X-RAY DIFFRACTION90.0613496933
3.3805-3.51590.3085397191741490.2266085550942855X-RAY DIFFRACTION92.6302806044
3.5159-3.67580.2256218355931540.2057638228672925X-RAY DIFFRACTION94.5348480196
3.6758-3.86960.2308405966821590.1809751566622974X-RAY DIFFRACTION95.9865196078
3.8696-4.11190.2070000807981570.1669167065992968X-RAY DIFFRACTION96.2723351818
4.1119-4.42920.2153899034411610.1600935854063027X-RAY DIFFRACTION97.3732437385
4.4292-4.87450.1916834730191580.1578533726753057X-RAY DIFFRACTION97.8095527837
4.8745-5.57910.2266773594161630.1769059678833081X-RAY DIFFRACTION97.6226301535
5.5791-7.02570.2594494707051630.1840623925073080X-RAY DIFFRACTION96.2885985748
7.0257-49.177603180320.1754930157851660.1697738136363244X-RAY DIFFRACTION96.8474865095

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