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- PDB-7nge: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1)... -

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Basic information

Entry
Database: PDB / ID: 7nge
TitleCrystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / L-Trp metabolism / hemoprotein / dynamics loop
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 / N'-Formylkynurenine / PHOSPHATE ION / TRYPTOPHAN / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMirgaux, M. / Wouters, J.
CitationJournal: Int J Tryptophan Res / Year: 2021
Title: Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site.
Authors: Mirgaux, M. / Leherte, L. / Wouters, J.
History
DepositionFeb 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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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)188,34152
Polymers181,2044
Non-polymers7,13848
Water12,034668
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,11813
Polymers45,3011
Non-polymers1,81712
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)47,25314
Polymers45,3011
Non-polymers1,95213
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)47,35717
Polymers45,3011
Non-polymers2,05616
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)46,6148
Polymers45,3011
Non-polymers1,3137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.360, 114.670, 219.670
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
Components on special symmetry positions
IDModelComponents
11B-733-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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
Details: Monomer A / Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase

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Non-polymers , 8 types, 716 molecules

#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NFK / N'-Formylkynurenine / (2S)-2-amino-4-[2-(formylamino)phenyl]-4-oxobutanoic acid


Mass: 236.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.59 % / Description: Red rectangular crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15.4% PEG 3350 0.1M Phosphate buffer pH 6.0 Protein : 5mM HEPES pH 7.4, 200mM NaCl, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 5, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→46.87 Å / Num. obs: 91724 / % possible obs: 99.56 % / Redundancy: 12.2 % / Biso Wilson estimate: 46.98 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.2072 / Rpim(I) all: 0.06342 / Rrim(I) all: 0.217 / Net I/σ(I): 10.43
Reflection shellResolution: 2.301→2.384 Å / Redundancy: 11.6 % / Rmerge(I) obs: 2.655 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 8917 / CC1/2: 0.541 / CC star: 0.838 / Rpim(I) all: 0.8097 / Rrim(I) all: 2.778 / % possible all: 97.63

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A62

7a62


Resolution: 2.3→46.87 Å / SU ML: 0.2926 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 1958 2.14 %
Rwork0.215 89561 -
obs0.2162 91519 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11834 0 481 668 12983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009512593
X-RAY DIFFRACTIONf_angle_d1.125817048
X-RAY DIFFRACTIONf_chiral_restr0.05611821
X-RAY DIFFRACTIONf_plane_restr0.00662150
X-RAY DIFFRACTIONf_dihedral_angle_d16.88241718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.38651310.37366114X-RAY DIFFRACTION96.72
2.36-2.420.30851300.32016347X-RAY DIFFRACTION99.91
2.42-2.490.35461220.28966347X-RAY DIFFRACTION99.77
2.49-2.570.31191390.26586341X-RAY DIFFRACTION99.88
2.57-2.670.27431470.266363X-RAY DIFFRACTION99.94
2.67-2.770.30371380.22176332X-RAY DIFFRACTION99.72
2.77-2.90.2691430.21276390X-RAY DIFFRACTION99.79
2.9-3.050.29511350.20256383X-RAY DIFFRACTION99.94
3.05-3.240.24561660.20496346X-RAY DIFFRACTION99.71
3.24-3.490.2621470.19756407X-RAY DIFFRACTION99.79
3.49-3.850.26751310.18716431X-RAY DIFFRACTION99.83
3.85-4.40.26311400.17566473X-RAY DIFFRACTION99.92
4.4-5.540.25661460.20496515X-RAY DIFFRACTION99.87
5.54-46.870.25051430.22466772X-RAY DIFFRACTION99.45

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