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- PDB-8iok: Crystal structure of AtHPPD-CLJ507 complex -

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Basic information

Entry
Database: PDB / ID: 8iok
TitleCrystal structure of AtHPPD-CLJ507 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / Complex
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / identical protein binding / cytoplasm
Similarity search - Function
4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / 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
Similarity search - Domain/homology
: / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsDong, J. / Yang, G.-F. / Lin, H.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of human HPPD-NTBC complex
Authors: Dong, J. / Yang, G.-F. / Lin, H.-Y.
History
DepositionMar 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)46,4123
Polymers45,9531
Non-polymers4592
Water905
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8246
Polymers91,9052
Non-polymers9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3420 Å2
ΔGint-37 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.670, 84.251, 64.191
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 45952.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD, PDS1, At1g06570, F12K11.9
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P93836, 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: Chemical ChemComp-SYI / 6-[diethylcarbamoyl(methyl)amino]-N-(1-methyl-1,2,3,4-tetrazol-5-yl)-2-(trifluoromethyl)pyridine-3-carboxamide


Mass: 400.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19F3N8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris/Bicine pH 8.5, 15% (v/v) MPD, 15% (w/v) PEG 1000, 15% (w/v) PEG 3350, 0.03M NaBr, 0.03M NaF, 0.03M NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. obs: 27599 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2547 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.991→39.551 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 43.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 1379 5 %
Rwork0.2358 --
obs0.238 27599 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.991→39.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 29 5 2844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082905
X-RAY DIFFRACTIONf_angle_d1.0563949
X-RAY DIFFRACTIONf_dihedral_angle_d15.551694
X-RAY DIFFRACTIONf_chiral_restr0.06438
X-RAY DIFFRACTIONf_plane_restr0.006516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9912-2.06230.4421350.36892547X-RAY DIFFRACTION96
2.0623-2.14490.40081350.33262607X-RAY DIFFRACTION99
2.1449-2.24250.3481360.30882597X-RAY DIFFRACTION99
2.2425-2.36070.36231380.29122641X-RAY DIFFRACTION99
2.3607-2.50860.31851380.27512618X-RAY DIFFRACTION99
2.5086-2.70230.37511390.28032632X-RAY DIFFRACTION99
2.7023-2.97410.36241380.28452626X-RAY DIFFRACTION100
2.9741-3.40430.34641400.26222651X-RAY DIFFRACTION99
3.4043-4.28820.25611390.21532641X-RAY DIFFRACTION99
4.2882-39.5510.19611410.18392660X-RAY DIFFRACTION98

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