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- PDB-1ey2: HUMAN HOMOGENTISATE DIOXYGENASE WITH FE(II) -

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Basic information

Entry
Database: PDB / ID: 1ey2
TitleHUMAN HOMOGENTISATE DIOXYGENASE WITH FE(II)
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 / tyrosine catabolic process / L-phenylalanine catabolic process / extracellular exosome / identical protein binding / metal ion 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 / Resolution: 2.3 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 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7042
Polymers53,6491
Non-polymers561
Water4,179232
1
A: HOMOGENTISATE 1,2-DIOXYGENASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)322,22712
Polymers321,8916
Non-polymers3356
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 area46080 Å2
ΔGint-246 kcal/mol
Surface area77820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.809, 157.809, 95.147
Angle α, β, γ (deg.)90., 90., 120.
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a hexamer constructed from two-fold and three-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: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Ammonium Sulfate, Imidazole, FeSO4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 31910 / Num. obs: 31495 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.412 / Num. unique all: 2801 / % possible all: 89.9
Reflection
*PLUS
Num. measured all: 187375
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 89.9 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→30 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1579 -RANDOM
Rwork0.193 ---
all0.193 31486 --
obs0.193 31486 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 1 232 3544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.93
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.9 Å2

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