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- PDB-6e45: CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) f... -

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Basic information

Entry
Database: PDB / ID: 6.0E+45
TitleCRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) free enzyme in the ferrous state
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / IDO1 / free enzyme / ferrous state
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 / PHOSPHATE ION / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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

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)184,41516
Polymers181,2044
Non-polymers3,21112
Water18,8621047
1
A: 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
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0123
Polymers45,3011
Non-polymers7112
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)45,9172
Polymers45,3011
Non-polymers6161
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)46,3847
Polymers45,3011
Non-polymers1,0836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.969, 196.538, 116.207
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1047 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→65.878 Å / Num. obs: 123961 / % possible obs: 99.4 % / Redundancy: 4.947 % / Biso Wilson estimate: 30.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.105 / Χ2: 1.141 / Net I/σ(I): 10.55 / Num. measured all: 613205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.124.8250.8021.88192730.790.90196.8
2.12-2.265.1380.5233.06187510.8940.58399.9
2.26-2.455.0580.3354.62174840.9550.374100
2.45-2.684.820.2116.83161390.9820.23799.9
2.68-2.994.8430.13310.12146540.9920.15100
2.99-3.465.1410.07916.23129780.9970.088100
3.46-4.235.0380.04924.78110370.9980.055100
4.23-5.974.6920.04127.3686390.9980.04699.9
5.97-65.8784.7580.03230.7750060.9990.03799.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2→65.878 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.27
RfactorNum. reflection% reflection
Rfree0.2258 1862 1.5 %
Rwork0.1886 --
obs0.1891 123872 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.33 Å2 / Biso mean: 33.5063 Å2 / Biso min: 15.89 Å2
Refinement stepCycle: final / Resolution: 2→65.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11690 0 217 1047 12954
Biso mean--34.54 39.36 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112203
X-RAY DIFFRACTIONf_angle_d1.04716567
X-RAY DIFFRACTIONf_chiral_restr0.2631793
X-RAY DIFFRACTIONf_plane_restr0.0062101
X-RAY DIFFRACTIONf_dihedral_angle_d19.7624450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9975-2.05150.29931350.28848705884093
2.0515-2.11190.28761440.259693449488100
2.1119-2.180.27231420.236293029444100
2.18-2.25790.29021420.227993249466100
2.2579-2.34840.26451420.217994209562100
2.3484-2.45520.2371440.212693299473100
2.4552-2.58470.22311430.205694239566100
2.5847-2.74660.28151420.198193709512100
2.7466-2.95870.21791440.199294329576100
2.9587-3.25640.23781450.198394279572100
3.2564-3.72760.18721430.171195189661100
3.7276-4.69620.19941480.144595929740100
4.6962-65.91330.19891480.16899824997299

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