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- PDB-1eyb: CRYSTAL STRUCTURE OF APO HUMAN HOMOGENTISATE DIOXYGENASE -

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Basic information

Entry
Database: PDB / ID: 1eyb
TitleCRYSTAL STRUCTURE OF APO HUMAN HOMOGENTISATE DIOXYGENASE
ComponentsHOMOGENTISATE 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / jelly roll / beta sandwich
Function / homology
Function and homology information


homogentisate 1,2-dioxygenase / homogentisate 1,2-dioxygenase activity / Tyrosine catabolism / L-tyrosine catabolic process / L-phenylalanine catabolic process / extracellular exosome / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Homogentisate 1,2-dioxygenase / Homogentisate 1,2-dioxygenase, C-terminal domain / Homogentisate 1,2-dioxygenase, N-terminal domain / Homogentisate 1,2-dioxygenase C-terminal / Homogentisate 1,2-dioxygenase N-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Homogentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsTimm, D.E. / Titus, G.P. / Penalva, M.A. / Mueller, H.A. / de Cordoba, S.M.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of human homogentisate dioxygenase.
Authors: Titus, G.P. / Mueller, H.A. / Burgner, J. / Rodriguez De Cordoba, S. / Penalva, M.A. / Timm, D.E.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 24, 2015Group: Data collection
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HOMOGENTISATE 1,2-DIOXYGENASE


Theoretical massNumber of molelcules
Total (without water)53,6491
Polymers53,6491
Non-polymers00
Water8,701483
1
A: HOMOGENTISATE 1,2-DIOXYGENASE
x 6


Theoretical massNumber of molelcules
Total (without water)321,8916
Polymers321,8916
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area44340 Å2
ΔGint-175 kcal/mol
Surface area80600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.380, 158.380, 93.459
Angle α, β, γ (deg.)90., 90., 120.
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a hexamer constructed from 2-fold and 3-fold crystallographic operations on the asymmetric unit.

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Components

#1: Protein HOMOGENTISATE 1,2-DIOXYGENASE


Mass: 53648.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: Q93099, homogentisate 1,2-dioxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Ammonium sulfate, imidazole, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown / PH range low: 7.4 / PH range high: 6.7
Components of the solutions
*PLUS
Conc.: 1.5-2.0 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 50741 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.292 / Num. unique all: 9772 / % possible all: 94.5
Reflection
*PLUS
Num. obs: 96251 / Num. measured all: 503991
Reflection shell
*PLUS
% possible obs: 94.5 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
RefinementResolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PROTIN
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2581 -Random
Rwork0.192 ---
all0.192 50741 --
obs0.192 50741 93 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 0 483 3786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0008
X-RAY DIFFRACTIONx_angle_deg1.65
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.3 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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