[English] 日本語
Yorodumi
- PDB-7a62: Structure of human indoleamine-2,3-dioxygenase 1 (hIDO1) with a c... -

+
Open data


ID or keywords:

Loading...

-
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 / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / positive regulation of T cell apoptotic process / negative regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / T cell proliferation / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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 / Heme B


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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more