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- PDB-6e41: CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) i... -

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Basic information

Entry
Database: PDB / ID: 6.0E+41
TitleCRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) in complex with ferric heme and an Epacadostat analog
ComponentsIndoleamine 2,3-dioxygenase 1
Keywordsoxidoreductase/oxidoreductase inhibitor / IDO1 / Epacadostat analog / inhibitor complex / oxidoreductase-oxidoreductase inhibitor complex
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 / Chem-HQS / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.291 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)186,40114
Polymers181,2044
Non-polymers5,19810
Water5,152286
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8284
Polymers45,3011
Non-polymers1,5273
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)46,3733
Polymers45,3011
Non-polymers1,0722
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)46,8284
Polymers45,3011
Non-polymers1,5273
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)46,3733
Polymers45,3011
Non-polymers1,0722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.916, 201.722, 114.893
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HQS / N-(3-bromo-4-fluorophenyl)-N'-hydroxy-4-{[2-(sulfamoylamino)ethyl]sulfanyl}-1,2,5-oxadiazole-3-carboximidamide


Mass: 455.283 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12BrFN6O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
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: 2.29→55.25 Å / Num. obs: 83301 / % possible obs: 97.7 % / Redundancy: 4.911 % / Biso Wilson estimate: 42.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.107 / Χ2: 1.218 / Net I/σ(I): 9.68 / Num. measured all: 409102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.29-2.435.080.7031.82126380.8440.78492.9
2.43-2.65.0470.4812.72125960.9190.53798.3
2.6-2.814.730.3164.13117650.9640.35598.2
2.81-3.074.8630.2036.48108560.9850.22798.7
3.07-3.435.0450.12210.698710.9940.13598.6
3.43-3.964.9940.07716.7587630.9960.08598.6
3.96-4.854.7540.05821.5274980.9980.06599.1
4.85-6.834.6150.05321.0258830.9970.05998.9
6.83-55.254.8180.03727.3334310.9990.04198.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.291→55.25 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 4121 4.96 %
Rwork0.2031 79030 -
obs0.2055 83151 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.61 Å2 / Biso mean: 48.4843 Å2 / Biso min: 26.17 Å2
Refinement stepCycle: final / Resolution: 2.291→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11888 0 322 286 12496
Biso mean--50.49 46.85 -
Num. residues----1507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01512552
X-RAY DIFFRACTIONf_angle_d1.33517064
X-RAY DIFFRACTIONf_chiral_restr0.071827
X-RAY DIFFRACTIONf_plane_restr0.0082159
X-RAY DIFFRACTIONf_dihedral_angle_d23.6184578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2913-2.31830.3629960.30672063215974
2.3183-2.34650.3511430.29332655279898
2.3465-2.37620.3371530.2962710286398
2.3762-2.40750.32051500.28752694284498
2.4075-2.44050.31391330.28052728286198
2.4405-2.47530.34081380.27412701283999
2.4753-2.51230.33631170.26872767288498
2.5123-2.55150.32091490.2682672282198
2.5515-2.59340.34541380.27262733287199
2.5934-2.63810.30551420.25212726286899
2.6381-2.68610.31481470.24552718286598
2.6861-2.73770.27691330.24472714284798
2.7377-2.79360.27361280.23282760288898
2.7936-2.85430.29931320.24212710284299
2.8543-2.92070.27941510.23832734288598
2.9207-2.99380.23871310.22562750288199
2.9938-3.07470.29561550.22852708286398
3.0747-3.16520.32431270.22692749287699
3.1652-3.26730.26881610.23152747290898
3.2673-3.38410.27781410.22042734287598
3.3841-3.51960.27681340.21222786292099
3.5196-3.67970.25651660.20222760292699
3.6797-3.87370.22721430.17962740288398
3.8737-4.11630.21131750.16492750292599
4.1163-4.4340.19951520.15562787293999
4.434-4.880.20471700.1542781295199
4.88-5.58550.22471390.17012827296699
5.5855-7.03490.22211410.18342870301199
7.0349-55.26580.17341360.15492956309297

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