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- PDB-5ec3: Structural insight into the catalyitc mechanism of human 4-Hydrox... -

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Basic information

Entry
Database: PDB / ID: 5ec3
TitleStructural insight into the catalyitc mechanism of human 4-Hydroxyphenylpyruvate dioxygenase
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / 4-Hydroxyphenylpyruvate dioxygenase / drug discovery
Function / homology
Function and homology information


Tyrosine catabolism / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / Golgi membrane / endoplasmic reticulum membrane / protein homodimerization activity / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. ...Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsYang, W.C. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation of China21332004 China
CitationJournal: To be published
Title: Structural insight into the catalyitc mechanism of human 4-Hydroxyphenylpyruvate dioxygenase
Authors: Yang, W.C. / Yang, G.F.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0552
Polymers44,9961
Non-polymers591
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-14 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.540, 98.540, 87.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase / / 4-hydroxyphenylpyruvic acid oxidase / HPPDase


Mass: 44996.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPD, PPD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: P32754, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris Propane, 0.2 M Sodium Acetate, 10% Ethylene Glycol, 18% PEG3,350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97961 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.1→49.2 Å / Num. obs: 114945 / % possible obs: 98.3 % / Redundancy: 5.1 % / Net I/σ(I): 9.3
Reflection shellHighest resolution: 2.1 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.3 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMACdata scaling
REFMACphasing
REFMACdata reduction
PHENIX1.8.2_1309refinement
RefinementResolution: 2.1→42.905 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 1454 5.11 %
Rwork0.1542 --
obs0.1561 28451 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 1 267 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073169
X-RAY DIFFRACTIONf_angle_d1.1214289
X-RAY DIFFRACTIONf_dihedral_angle_d13.6221194
X-RAY DIFFRACTIONf_chiral_restr0.079457
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.29351530.22542586X-RAY DIFFRACTION97
2.1751-2.26220.21031570.17862653X-RAY DIFFRACTION98
2.2622-2.36510.20771550.16142629X-RAY DIFFRACTION97
2.3651-2.48980.20081460.15842713X-RAY DIFFRACTION99
2.4898-2.64580.22331520.15182671X-RAY DIFFRACTION99
2.6458-2.850.16921270.1462741X-RAY DIFFRACTION99
2.85-3.13680.18961340.14612761X-RAY DIFFRACTION100
3.1368-3.59050.17221450.13452736X-RAY DIFFRACTION100
3.5905-4.52280.14861410.13542767X-RAY DIFFRACTION99
4.5228-42.91350.21431440.17242740X-RAY DIFFRACTION95

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