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- PDB-7p0r: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) co... -

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Basic information

Entry
Database: PDB / ID: 7p0r
TitleCrystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) complex with the JK-loop refined in the intermediate conformation
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / L-TRP METABOLISM / HEMOPROTEIN / DYNAMICS LOOP
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 / L-tryptophan catabolic process to kynurenine / 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 / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / positive regulation of type 2 immune response / L-tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive 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 / 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 / N'-Formylkynurenine / PHOSPHATE ION / TRYPTOPHAN / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMirgaux, M. / Wouters, J.
CitationJournal: Int J Tryptophan Res / Year: 2021
Title: Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site.
Authors: Mirgaux, M. / Leherte, L. / Wouters, J.
History
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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)186,51332
Polymers181,2044
Non-polymers5,30928
Water8,953497
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6178
Polymers45,3011
Non-polymers1,3167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88410
Polymers45,3011
Non-polymers1,5839
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6148
Polymers45,3011
Non-polymers1,3137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3986
Polymers45,3011
Non-polymers1,0975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.890, 115.720, 217.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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Protein , 1 types, 4 molecules ABCD

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pet28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase

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Non-polymers , 6 types, 525 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NFK / N'-Formylkynurenine / (2S)-2-amino-4-[2-(formylamino)phenyl]-4-oxobutanoic acid


Mass: 236.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Phosphate buffer 15.4% PEG 3350 Protein buffer : 5mM Hepes, 200 mM NaCl, 5 mM DTT Cryoprotection : 20% glycerol, 20 mM sodium dithionite
PH range: 6.0-6.4 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 5, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 2.5→49.22 Å / Num. obs: 71454 / % possible obs: 99.65 % / Redundancy: 7.21 % / Biso Wilson estimate: 54.62 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 7.21
Reflection shellResolution: 2.5→2.589 Å / Mean I/σ(I) obs: 0.79 / Num. unique obs: 7008 / CC1/2: 0.59 / CC star: 0.861 / % possible all: 99.42

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
MxCuBEdata collection
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A62

7a62


Resolution: 2.5→49.22 Å / SU ML: 0.3843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2851 3562 4.99 %
Rwork0.218 67759 -
obs0.2213 71321 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11891 0 362 497 12750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009512538
X-RAY DIFFRACTIONf_angle_d1.081917000
X-RAY DIFFRACTIONf_chiral_restr0.05161826
X-RAY DIFFRACTIONf_plane_restr0.012156
X-RAY DIFFRACTIONf_dihedral_angle_d18.84891693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.41721320.39172513X-RAY DIFFRACTION92.68
2.53-2.570.43681410.36352676X-RAY DIFFRACTION99.89
2.57-2.610.42771420.36452682X-RAY DIFFRACTION99.79
2.61-2.650.41491400.34122650X-RAY DIFFRACTION99.79
2.65-2.690.38541420.32842712X-RAY DIFFRACTION99.44
2.69-2.740.42321410.31112668X-RAY DIFFRACTION99.72
2.74-2.790.35511410.28122705X-RAY DIFFRACTION99.82
2.79-2.840.35341400.28032655X-RAY DIFFRACTION99.89
2.84-2.90.341430.27192730X-RAY DIFFRACTION99.9
2.9-2.960.35061400.26512662X-RAY DIFFRACTION99.86
2.96-3.030.3161410.2482697X-RAY DIFFRACTION99.68
3.03-3.110.28271430.25222721X-RAY DIFFRACTION99.69
3.11-3.190.30921410.25152668X-RAY DIFFRACTION99.61
3.19-3.280.34641420.24262723X-RAY DIFFRACTION99.79
3.28-3.390.32161420.21122711X-RAY DIFFRACTION99.76
3.39-3.510.26981420.20252717X-RAY DIFFRACTION99.65
3.51-3.650.2551410.19182692X-RAY DIFFRACTION99.75
3.65-3.820.2651440.18042725X-RAY DIFFRACTION99.69
3.82-4.020.27711420.18482725X-RAY DIFFRACTION99.72
4.02-4.270.23161440.17982736X-RAY DIFFRACTION99.76
4.27-4.60.26751440.18332723X-RAY DIFFRACTION99.79
4.6-5.060.24271450.18132780X-RAY DIFFRACTION99.83
5.06-5.790.2951460.2092767X-RAY DIFFRACTION99.83
5.79-7.290.25831480.20862806X-RAY DIFFRACTION99.86
7.29-49.220.21071550.18182915X-RAY DIFFRACTION98.62

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