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- PDB-6ubp: Crystal structure of a photochemical intermediate of human indole... -

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Basic information

Entry
Database: PDB / ID: 6ubp
TitleCrystal structure of a photochemical intermediate of human indoleamine 2,3-dioxygenase 1 in complex with carbon monoxide and tryptophan
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / human Indoleamine 2 / 3-dioxygenase x-ray photolysis of CO and Tryptophan
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPham, K.N. / Yeh, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115773 United States
National Science Foundation (NSF, United States)CHE-1404929 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Conformational Plasticity in Human Heme-Based Dioxygenases.
Authors: Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R.
History
DepositionSep 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2818
Polymers95,5842
Non-polymers1,6976
Water1,13563
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6414
Polymers47,7921
Non-polymers8493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6414
Polymers47,7921
Non-polymers8493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.944, 97.727, 130.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Indoleamine 2,3-dioxygenase 1 / / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 47791.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli (E. coli) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 10
Details: 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.95→29.34 Å / Num. obs: 24106 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.2
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 8 % / Rmerge(I) obs: 2.015 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3854 / CC1/2: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WMU

5wmu


Resolution: 2.95→29.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.175 / SU ML: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1165 4.8 %RANDOM
Rwork0.2152 ---
obs0.2175 22893 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.05 Å2 / Biso mean: 102.551 Å2 / Biso min: 67.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å2-0 Å2
2---3.07 Å20 Å2
3---4.94 Å2
Refinement stepCycle: final / Resolution: 2.95→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5932 0 120 63 6115
Biso mean--108.32 87.61 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175798
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.6618420
X-RAY DIFFRACTIONr_angle_other_deg1.0341.58913455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74722.656305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.455151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0621532
X-RAY DIFFRACTIONr_chiral_restr0.0410.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026872
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021308
LS refinement shellResolution: 2.95→3.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 87 -
Rwork0.373 1670 -
all-1757 -
obs--100 %

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