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- PDB-6e44: CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) f... -

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Basic information

Entry
Database: PDB / ID: 6.0E+44
TitleCRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) free enzyme in the ferric state
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / IDO1 / free enzyme / ferric 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
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: 1.903 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)183,95411
Polymers181,2044
Non-polymers2,7517
Water16,898938
1
A: 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
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)46,1074
Polymers45,3011
Non-polymers8063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.082, 196.995, 116.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-634-

HOH

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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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
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: 1.9→47.038 Å / Num. obs: 143553 / % possible obs: 99.4 % / Redundancy: 3.715 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.071 / Χ2: 1.203 / Net I/σ(I): 12.26 / Num. measured all: 533366
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.023.7980.6361.86228330.8170.74298.9
2.02-2.153.6540.363.43216300.9340.42399.6
2.15-2.333.7480.225.79202190.970.25799.7
2.33-2.553.8310.1418.77186820.9880.16499.9
2.55-2.853.5740.08912.6168600.9940.10599.2
2.85-3.293.8550.05818.98149790.9970.06899.8
3.29-4.023.5970.03827.06126800.9980.04598.9
4.02-5.673.6590.0332.8299420.9990.03699.2
5.67-47.0383.540.02434.1857280.9990.02898.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.903→47.038 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2347 2153 1.5 %
Rwork0.1941 --
obs0.1947 143441 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.87 Å2 / Biso mean: 35.3009 Å2 / Biso min: 16.86 Å2
Refinement stepCycle: final / Resolution: 1.903→47.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11699 0 187 938 12824
Biso mean--37.3 41.19 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112215
X-RAY DIFFRACTIONf_angle_d0.9816598
X-RAY DIFFRACTIONf_chiral_restr0.2031800
X-RAY DIFFRACTIONf_plane_restr0.0062108
X-RAY DIFFRACTIONf_dihedral_angle_d20.1844464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9027-1.9470.3441410.31389022916396
1.947-1.99570.35241410.297193739514100
1.9957-2.04970.29041410.265193749515100
2.0497-2.110.25891430.2489327947099
2.11-2.17810.29681440.23579329947399
2.1781-2.25590.25681420.22493719513100
2.2559-2.34620.24391450.210194319576100
2.3462-2.4530.27051420.209594279569100
2.453-2.58230.21651450.204494579602100
2.5823-2.74410.26661430.2019352949599
2.7441-2.9560.24721430.20349480962399
2.956-3.25340.25421450.19594739618100
3.2534-3.7240.20761480.17889521966999
3.724-4.69110.1831430.14919511965499
4.6911-47.05250.2141470.17449840998799

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