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- PDB-7z2l: Crystal structure of L-Kynurenine in the active site of human Ind... -

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Basic information

Entry
Database: PDB / ID: 7z2l
TitleCrystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1)
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Dioxygenase / Tryptophan metabolism
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 / 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 / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / OXYGEN MOLECULE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsMirgaux, M. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds de la Recherche Scientifique (FNRS) Belgium
CitationJournal: To Be Published
Title: Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1)
Authors: Mirgaux, M. / Wouters, J.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)185,94829
Polymers181,2044
Non-polymers4,74425
Water16,286904
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5868
Polymers45,3011
Non-polymers1,2857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7588
Polymers45,3011
Non-polymers1,4577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3187
Polymers45,3011
Non-polymers1,0176
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2866
Polymers45,3011
Non-polymers9855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.000, 116.280, 217.590
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

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P14902, indoleamine 2,3-dioxygenase

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Non-polymers , 5 types, 929 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: Red rectangular crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Well : 0.1M Phosphate buffer, pH= 6.2, PEG 3350 = 16% Protein: 5mM Hepes, 200mM NaCl, 5mM DTT
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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2021 / Details: channel-cut
RadiationMonochromator: channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.56→47.23 Å / Num. obs: 66614 / % possible obs: 99.18 % / Redundancy: 13.6 % / Biso Wilson estimate: 42.15 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.09638 / Net I/σ(I): 13.33
Reflection shellResolution: 2.562→2.654 Å / Mean I/σ(I) obs: 2.22 / Num. unique obs: 6308 / CC1/2: 0.855 / CC star: 0.96 / Rpim(I) all: 0.5299 / % possible all: 93.96

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Processing

Software
NameVersionClassification
XDS1.19.2_4158data reduction
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NGE

7nge


Resolution: 2.56→47.23 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2441 3316 4.99 %
Rwork0.1802 63102 -
obs0.1834 66418 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.4 Å2
Refinement stepCycle: LAST / Resolution: 2.56→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11813 0 326 904 13043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008712458
X-RAY DIFFRACTIONf_angle_d0.979316897
X-RAY DIFFRACTIONf_chiral_restr0.04941817
X-RAY DIFFRACTIONf_plane_restr0.00772149
X-RAY DIFFRACTIONf_dihedral_angle_d12.19391679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.60.37421160.31422255X-RAY DIFFRACTION85.81
2.6-2.640.30811370.26522600X-RAY DIFFRACTION99.74
2.64-2.680.2971380.24732615X-RAY DIFFRACTION99.93
2.68-2.720.3221380.23522613X-RAY DIFFRACTION99.75
2.72-2.770.32691380.23212627X-RAY DIFFRACTION99.86
2.77-2.820.29361360.22392574X-RAY DIFFRACTION99.82
2.82-2.870.30631380.21022617X-RAY DIFFRACTION99.93
2.87-2.930.30191380.21392632X-RAY DIFFRACTION99.82
2.93-30.30471380.20742605X-RAY DIFFRACTION99.85
3-3.070.25171380.20552622X-RAY DIFFRACTION99.78
3.07-3.140.30551390.20642637X-RAY DIFFRACTION99.78
3.14-3.230.30181380.20012615X-RAY DIFFRACTION99.42
3.23-3.320.25211390.18552624X-RAY DIFFRACTION99.86
3.32-3.430.26271370.17682625X-RAY DIFFRACTION99.64
3.43-3.550.21461380.16622619X-RAY DIFFRACTION99.93
3.55-3.690.23641400.15442648X-RAY DIFFRACTION99.93
3.69-3.860.22761380.15242651X-RAY DIFFRACTION99.93
3.86-4.070.23741400.1492651X-RAY DIFFRACTION99.82
4.07-4.320.17671390.1492644X-RAY DIFFRACTION99.93
4.32-4.650.20291410.14662676X-RAY DIFFRACTION100
4.65-5.120.20251410.14982675X-RAY DIFFRACTION99.96
5.12-5.860.23631430.18222708X-RAY DIFFRACTION99.93
5.86-7.380.25781430.19182732X-RAY DIFFRACTION99.9
7.38-47.230.19741450.16852837X-RAY DIFFRACTION98.68

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