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- PDB-2d0u: Crystal structure of cyanide bound form of human indoleamine 2,3-... -

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Basic information

Entry
Database: PDB / ID: 2d0u
TitleCrystal structure of cyanide bound form of human indoleamine 2,3-dioxygenase
ComponentsIndoleamine 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / helix bundle / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSugimoto, H. / Oda, S. / Otsuki, T. / Hino, T. / Yoshida, T. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase.
Authors: Sugimoto, H. / Oda, S. / Otsuki, T. / Hino, T. / Yoshida, T. / Shiro, Y.
History
DepositionAug 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Indoleamine 2,3-dioxygenase
B: Indoleamine 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,44710
Polymers91,3332
Non-polymers2,1148
Water00
1
A: Indoleamine 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7245
Polymers45,6661
Non-polymers1,0574
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7245
Polymers45,6661
Non-polymers1,0574
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.352, 97.089, 129.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsThe biological assembly is a monomer

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Components

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


Mass: 45666.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: P14902, EC: 1.13.11.42
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM

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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 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 8000, CHES, ammonium acetate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9785 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 14518 / Num. obs: 14518 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1430 / Rsym value: 0.341 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 3.4→19.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2248730.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 718 5 %RANDOM
Rwork0.213 ---
all0.249 14422 --
obs0.249 14422 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.23859 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.09 Å20 Å20 Å2
2---1.69 Å20 Å2
3---15.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3.4→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 142 0 6062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight Biso Weight position
11CONSTRX-RAY DIFFRACTION2400
22X-RAY DIFFRACTION4100
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 104 4.4 %
Rwork0.274 2274 -
obs--93.7 %

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