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- PDB-7p0n: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1)... -

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Basic information

Entry
Database: PDB / ID: 7p0n
TitleCrystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the open conformation
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / L-Trp metabolism / hemoprotein / dynamics loop
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / positive regulation of T cell apoptotic process / negative 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
PROTOPORPHYRIN IX CONTAINING FE / N'-Formylkynurenine / OXYGEN MOLECULE / PHOSPHATE ION / TRYPTOPHAN / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionJun 30, 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

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)187,51843
Polymers181,2044
Non-polymers6,31439
Water8,863492
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,83311
Polymers45,3011
Non-polymers1,53210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5029
Polymers45,3011
Non-polymers1,2018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,13313
Polymers45,3011
Non-polymers1,83212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,05010
Polymers45,3011
Non-polymers1,7499
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.360, 114.570, 220.980
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-682-

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
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pet28-a / Details (production host): Mutations K116A, K117A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase

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Non-polymers , 8 types, 531 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NFK / N'-Formylkynurenine / (2S)-2-amino-4-[2-(formylamino)phenyl]-4-oxobutanoic acid / N'-Formylkynurenine


Mass: 236.224 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.81 Å3/Da / Density % sol: 56.72 % / Description: Red rectangular crystal 0.3mm
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 14.5% PEG 3350 0.1M Phosphate buffer 2mM L-Trp Protein buffer : Hepes 5mM, 200mM NaCl, 5mM DTT Cryoprotection: 20 mM sodium dithionite, 20% glycerol
PH range: 6.0-6.4 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 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: 0.98012 Å / Relative weight: 1
ReflectionResolution: 2.5→49.29 Å / Num. obs: 71786 / % possible obs: 99.34 % / Redundancy: 7 % / Biso Wilson estimate: 52.26 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 6.7
Reflection shellResolution: 2.504→2.593 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 7022 / CC1/2: 0.606 / CC star: 0.869 / % possible all: 97.88

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A62

7a62


Resolution: 2.5→49.29 Å / SU ML: 0.3948 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 3582 5 %
Rwork0.2151 67997 -
obs0.2182 71579 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11782 0 429 492 12703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008812496
X-RAY DIFFRACTIONf_angle_d1.121416932
X-RAY DIFFRACTIONf_chiral_restr0.0531812
X-RAY DIFFRACTIONf_plane_restr0.00842149
X-RAY DIFFRACTIONf_dihedral_angle_d19.25931700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.45611300.40122487X-RAY DIFFRACTION95.09
2.54-2.570.37741360.36192569X-RAY DIFFRACTION99.59
2.57-2.610.40611370.34022595X-RAY DIFFRACTION99.67
2.61-2.650.41271370.32372589X-RAY DIFFRACTION99.67
2.65-2.690.33921350.31462559X-RAY DIFFRACTION99.41
2.69-2.730.36831380.29552609X-RAY DIFFRACTION99.42
2.73-2.780.37681340.28042561X-RAY DIFFRACTION99.63
2.78-2.830.29471380.26222616X-RAY DIFFRACTION99.71
2.83-2.880.32551370.25062597X-RAY DIFFRACTION99.53
2.88-2.940.31141360.23882590X-RAY DIFFRACTION99.82
2.94-3.010.33231370.23512602X-RAY DIFFRACTION99.75
3.01-3.080.32221370.22842583X-RAY DIFFRACTION99.71
3.08-3.150.28931380.22512616X-RAY DIFFRACTION99.39
3.15-3.240.29421360.22762582X-RAY DIFFRACTION99.31
3.24-3.330.24281370.21252597X-RAY DIFFRACTION99.71
3.33-3.440.291380.20392619X-RAY DIFFRACTION99.67
3.44-3.570.291390.19512629X-RAY DIFFRACTION99.71
3.57-3.710.26171380.18122623X-RAY DIFFRACTION99.57
3.71-3.880.25371370.1752610X-RAY DIFFRACTION99.38
3.88-4.080.23991390.17252621X-RAY DIFFRACTION99.42
4.08-4.340.21961350.1692616X-RAY DIFFRACTION99.42
4.34-4.670.23731400.18182653X-RAY DIFFRACTION99.68
4.67-5.140.23391410.18552670X-RAY DIFFRACTION99.68
5.14-5.880.28781410.22292672X-RAY DIFFRACTION99.5
5.88-7.410.29561420.22612722X-RAY DIFFRACTION99.65
7.41-49.290.25081490.20242810X-RAY DIFFRACTION98.6

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