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- PDB-4hka: Crystal structure of Drosophila melanogaster tryptophan 2,3-dioxy... -

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Basic information

Entry
Database: PDB / ID: 4hka
TitleCrystal structure of Drosophila melanogaster tryptophan 2,3-dioxygenase in complex with HEME
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / kynurenine pathway / catalytic mechanism / regulatory mechanism
Function / homology
Function and homology information


compound eye pigmentation / Tryptophan catabolism / ommochrome biosynthetic process / tryptophan catabolic process to acetyl-CoA / : / tryptophan 2,3-dioxygenase / kynurenine metabolic process / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / tryptophan catabolic process ...compound eye pigmentation / Tryptophan catabolism / ommochrome biosynthetic process / tryptophan catabolic process to acetyl-CoA / : / tryptophan 2,3-dioxygenase / kynurenine metabolic process / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / tryptophan catabolic process / protein homotetramerization / heme binding / metal ion binding
Similarity search - Function
Helix Hairpins - #3810 / Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / Tryptophan/Indoleamine 2,3-dioxygenase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuang, W. / Ding, J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of Drosophila melanogaster tryptophan 2,3-dioxygenase reveals insights into substrate recognition and catalytic mechanism.
Authors: Huang, W. / Gong, Z. / Li, J. / Ding, J.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9782
Polymers43,3621
Non-polymers6161
Water43224
1
A: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,9138
Polymers173,4474
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area27450 Å2
ΔGint-199 kcal/mol
Surface area55030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.719, 114.719, 213.438
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

#1: Protein Tryptophan 2,3-dioxygenase / TDO / Protein vermilion / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / ...TDO / Protein vermilion / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / Tryptophan pyrrolase / Tryptophanase


Mass: 43361.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: v, CG5163 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P20351, tryptophan 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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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: 4.67 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, and 1.1 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 23131 / % possible obs: 97.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 30.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 4.7 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.372 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1154 5 %RANDOM
Rwork0.2258 ---
obs0.2276 23000 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.97 Å2 / Biso mean: 72.5897 Å2 / Biso min: 42.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å21.53 Å20 Å2
2--3.05 Å20 Å2
3----4.58 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 43 24 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192983
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.9894038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0075344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13823.419155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91115548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4351529
X-RAY DIFFRACTIONr_chiral_restr0.0660.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212268
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 89 -
Rwork0.299 1409 -
all-1498 -
obs--98.49 %

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