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- PDB-7e0x: Crystal structure of Arabidopsis thaliana HPPD complexed with 4-h... -

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Basic information

Entry
Database: PDB / ID: 7e0x
TitleCrystal structure of Arabidopsis thaliana HPPD complexed with 4-hydroxyphenylacetic acid
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Enzyme / Complex / Intermediate product
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / L-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-HYDROXYPHENYLACETATE / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.887 Å
AuthorsLin, H.Y. / Yang, G.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study.
Authors: Lin, H.Y. / Chen, X. / Dong, J. / Yang, J.F. / Xiao, H. / Ye, Y. / Li, L.H. / Zhan, C.G. / Yang, W.C. / Yang, G.F.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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)44,9953
Polymers44,7841
Non-polymers2112
Water2,360131
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9916
Polymers89,5692
Non-polymers4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4440 Å2
ΔGint-29 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.026, 83.889, 62.753
Angle α, β, γ (deg.)90.00, 99.95, 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: 44784.332 Da / Num. of mol.: 1 / Mutation: S267W
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 (E. coli)
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4HP / 4-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.38 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaAc pH4.5, 33% PEG 400, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9775 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.887→30 Å / Num. obs: 30147 / % possible obs: 96.6 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.447 / Num. unique obs: 1498 / CC1/2: 0.869 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YY6

5yy6


Resolution: 1.887→28.683 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1431 4.75 %
Rwork0.2049 --
obs0.2066 30121 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.887→28.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 12 131 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072988
X-RAY DIFFRACTIONf_angle_d0.8244050
X-RAY DIFFRACTIONf_dihedral_angle_d21.6941058
X-RAY DIFFRACTIONf_chiral_restr0.054446
X-RAY DIFFRACTIONf_plane_restr0.006529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.887-1.95420.37211300.31842498X-RAY DIFFRACTION83
1.9542-2.03250.35891490.31252928X-RAY DIFFRACTION97
2.0325-2.12490.35171320.30842838X-RAY DIFFRACTION95
2.1249-2.23690.31471460.27262847X-RAY DIFFRACTION95
2.2369-2.3770.27431380.23672967X-RAY DIFFRACTION99
2.377-2.56040.25851790.22572949X-RAY DIFFRACTION98
2.5604-2.81790.29491370.20822954X-RAY DIFFRACTION98
2.8179-3.22520.22451430.19732848X-RAY DIFFRACTION94
3.2252-4.06160.19651460.17192977X-RAY DIFFRACTION98
4.0616-28.6830.20571310.17462884X-RAY DIFFRACTION93

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