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- PDB-7yxt: Crystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) ... -

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Basic information

Entry
Database: PDB / ID: 7yxt
TitleCrystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) with different conformations for G261-G265 fragment
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Dioxygenase / Tryptophan metabolism
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 / OXYGEN MOLECULE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMirgaux, M. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds de la Recherche Scientifique (FNRS) Belgium
CitationJournal: To Be Published
Title: Crystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) with different conformations for G261-G265 fragment
Authors: Mirgaux, M. / Wouters, J.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)184,53018
Polymers181,2044
Non-polymers3,32714
Water12,358686
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)46,2866
Polymers45,3011
Non-polymers9855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0093
Polymers45,3011
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2266
Polymers45,3011
Non-polymers9255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.040, 117.610, 217.180
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

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pet-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14902, indoleamine 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Well: 0.1M KH2PO4/K2HPO4 buffer at pH 6.2 supplemented with 17% of PEG 3350 solution Protein: 5 mM HEPES/NaOH pH 7.6, 200 mM NaCl, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.48→49.07 Å / Num. obs: 73894 / % possible obs: 99.71 % / Redundancy: 13.3 % / Biso Wilson estimate: 48.89 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1683 / Rpim(I) all: 0.04815 / Rrim(I) all: 0.1751 / Net I/σ(I): 11.01
Reflection shellResolution: 2.485→2.574 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 7203 / CC1/2: 0.802 / CC star: 0.943 / Rpim(I) all: 0.4084 / % possible all: 98.66

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NGE

7nge


Resolution: 2.48→49.07 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 3694 5.01 %
Rwork0.1963 70104 -
obs0.1993 73798 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.24 Å2
Refinement stepCycle: LAST / Resolution: 2.48→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11881 0 228 686 12795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008612445
X-RAY DIFFRACTIONf_angle_d1.005916888
X-RAY DIFFRACTIONf_chiral_restr0.0491821
X-RAY DIFFRACTIONf_plane_restr0.00782153
X-RAY DIFFRACTIONf_dihedral_angle_d10.24561676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.520.36011350.29942566X-RAY DIFFRACTION96.6
2.52-2.550.34651410.28432673X-RAY DIFFRACTION100
2.55-2.590.3431400.27882648X-RAY DIFFRACTION99.89
2.59-2.630.32231410.27632689X-RAY DIFFRACTION99.93
2.63-2.670.33991390.26592639X-RAY DIFFRACTION99.96
2.67-2.710.27351430.25092705X-RAY DIFFRACTION99.72
2.71-2.760.30741400.25282651X-RAY DIFFRACTION99.86
2.76-2.810.32171400.23612662X-RAY DIFFRACTION99.86
2.81-2.860.28021410.2272676X-RAY DIFFRACTION99.96
2.86-2.920.30241390.22212662X-RAY DIFFRACTION99.89
2.92-2.980.29441430.22062707X-RAY DIFFRACTION99.89
2.98-3.050.27981380.22082637X-RAY DIFFRACTION99.89
3.05-3.130.33931430.23712708X-RAY DIFFRACTION99.89
3.13-3.220.30261410.24112665X-RAY DIFFRACTION99.75
3.22-3.310.30191410.22782676X-RAY DIFFRACTION99.86
3.31-3.420.29141420.20422695X-RAY DIFFRACTION99.86
3.42-3.540.2521410.19472689X-RAY DIFFRACTION99.82
3.54-3.680.25271430.18192718X-RAY DIFFRACTION99.97
3.68-3.850.21781420.17982693X-RAY DIFFRACTION99.93
3.85-4.050.2541430.17142714X-RAY DIFFRACTION99.97
4.05-4.30.22731430.15862707X-RAY DIFFRACTION99.93
4.3-4.640.23981440.1612730X-RAY DIFFRACTION100
4.64-5.10.22011440.15882752X-RAY DIFFRACTION99.97
5.1-5.840.22451450.18062742X-RAY DIFFRACTION99.97
5.84-7.350.27711470.19182804X-RAY DIFFRACTION99.9
7.35-49.070.18651550.1662896X-RAY DIFFRACTION99.03

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