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- PDB-6e43: Crystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) i... -

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Basic information

Entry
Database: PDB / ID: 6.0E+43
TitleCrystal structure of human indoleamine 2,3-dioxygenase 1 (IDO1) in complex with a BMS-978587 analog
ComponentsIndoleamine 2,3-dioxygenase 1
Keywordsoxidoreductase/oxidoreductase inhibitor / IDO1 / BMS-978587 analog / inhibitor complex / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / 'de novo' NAD+ biosynthetic process from L-tryptophan / positive regulation of type 2 immune response / L-tryptophan catabolic process / negative regulation of T cell apoptotic process / Tryptophan catabolism / 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 / 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
BENZOIC ACID / Chem-HQM / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.705 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form.
Authors: Luo, S. / Xu, K. / Xiang, S. / Chen, J. / Chen, C. / Guo, C. / Tong, Y. / Tong, L.
History
DepositionJul 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)183,54712
Polymers181,2044
Non-polymers2,3438
Water22,5731253
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8873
Polymers45,3011
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8873
Polymers45,3011
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8873
Polymers45,3011
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8873
Polymers45,3011
Non-polymers5862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.481, 195.388, 118.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / Fragment: residue 15-403 / 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 (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical
ChemComp-HQM / (1R,2S)-2-(4-[cyclohexyl(2-methylpropyl)amino]-3-{[(4-methylphenyl)carbamoyl]amino}phenyl)cyclopropane-1-carboxylic acid


Mass: 463.612 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H37N3O3
#3: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1253 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.2 / Details: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.705→47.642 Å / Num. obs: 201224 / % possible obs: 99.2 % / Redundancy: 4.435 % / Biso Wilson estimate: 28.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.071 / Χ2: 1.128 / Net I/σ(I): 11.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.71-1.814.3550.8251.46320250.7210.94198.7
1.81-1.934.5220.4452.84304460.9080.50699.6
1.93-2.094.4980.2365.27283780.9680.26899.6
2.09-2.294.3320.1358.8260700.9870.15599.3
2.29-2.564.6030.08713.56237620.9940.09999.7
2.56-2.954.3320.06318.19209510.9950.07299.3
2.95-3.614.550.04925.03178380.9970.05699.3
3.61-5.094.270.04229.78137960.9970.04898.2
5.09-47.6424.3360.03930.6779580.9970.04598.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.705→47.642 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.62
RfactorNum. reflection% reflection
Rfree0.2306 3011 1.5 %
Rwork0.1938 --
obs0.1943 201103 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.17 Å2 / Biso mean: 33.019 Å2 / Biso min: 15.06 Å2
Refinement stepCycle: final / Resolution: 1.705→47.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11782 0 172 1253 13207
Biso mean--28.29 40.16 -
Num. residues----1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712286
X-RAY DIFFRACTIONf_angle_d0.916643
X-RAY DIFFRACTIONf_chiral_restr0.1721827
X-RAY DIFFRACTIONf_plane_restr0.0062132
X-RAY DIFFRACTIONf_dihedral_angle_d23.4764552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.705-1.73170.32781300.32288587871796
1.7317-1.76010.31671370.301189679104100
1.7601-1.79040.29071370.281289969133100
1.7904-1.8230.31871350.268389409075100
1.823-1.85810.28771360.250689829118100
1.8581-1.8960.27241360.242889269062100
1.896-1.93720.28921370.25688994913199
1.9372-1.98230.26661360.243489739109100
1.9823-2.03190.28511370.227389939130100
2.0319-2.08680.26041360.22178973910999
2.0868-2.14820.24191370.21048939907699
2.1482-2.21750.24051360.20828995913199
2.2175-2.29680.25621370.21228979911699
2.2968-2.38870.23921360.208590089144100
2.3887-2.49750.25141370.206590499186100
2.4975-2.62910.23221420.204990459187100
2.6291-2.79380.24171290.19849011914099
2.7938-3.00950.23631400.199390599199100
3.0095-3.31230.22691360.186891159251100
3.3123-3.79140.19011420.17099069921199
3.7914-4.77610.19821370.14699084922198
4.7761-47.66040.20741450.16859408955398

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