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- PDB-5xgk: Crystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate... -

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Basic information

Entry
Database: PDB / ID: 5xgk
TitleCrystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (AtHPPD) complexed with its substrate 4-hydroxyphenylpyruvate acid (HPPA)
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / 4-Hydroxyphenylpyruvate Dioxygenase / catalytic mechanism / drug discovery
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 / 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 ...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
ACETATE ION / : / (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, G.F. / Yang, W.C. / Lin, H.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21332004 China
National Natural Science Foundation of China21672079 China
CitationJournal: Res / Year: 2019
Title: Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery.
Authors: Lin, H.Y. / Chen, X. / Chen, J.N. / Wang, D.W. / Wu, F.X. / Lin, S.Y. / Zhan, C.G. / Wu, J.W. / Yang, W.C. / Yang, G.F.
History
DepositionApr 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.page_first ..._citation.country / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,13713
Polymers195,4954
Non-polymers6429
Water3,819212
1
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2198
Polymers97,7482
Non-polymers4716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-25 kcal/mol
Surface area28360 Å2
MethodPISA
2
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9185
Polymers97,7482
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-36 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.606, 95.294, 98.000
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48873.832 Da / Num. of mol.: 4
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(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-TYF / (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid


Mass: 182.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O4
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M NaAc, 0.1M NaCl, 36% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97961 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 42651 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.117 / Net I/σ(I): 8.19
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 2170 / CC1/2: 0.828 / Rpim(I) all: 0.312

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TFZ

1tfz


Resolution: 2.8→44.24 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3121 2165 5.08 %
Rwork0.2583 --
obs0.261 42651 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11102 0 33 212 11347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411390
X-RAY DIFFRACTIONf_angle_d0.96515402
X-RAY DIFFRACTIONf_dihedral_angle_d11.0094004
X-RAY DIFFRACTIONf_chiral_restr0.0321712
X-RAY DIFFRACTIONf_plane_restr0.0032008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86510.38341440.28232714X-RAY DIFFRACTION100
2.8651-2.93680.38961820.2732684X-RAY DIFFRACTION100
2.9368-3.01610.33251490.26942695X-RAY DIFFRACTION99
3.0161-3.10490.33371330.26052736X-RAY DIFFRACTION99
3.1049-3.20510.34261470.27162734X-RAY DIFFRACTION100
3.2051-3.31960.30241640.26062696X-RAY DIFFRACTION99
3.3196-3.45240.31941340.25442724X-RAY DIFFRACTION99
3.4524-3.60950.31941430.24522716X-RAY DIFFRACTION99
3.6095-3.79970.32241330.23942738X-RAY DIFFRACTION99
3.7997-4.03760.27131330.23652723X-RAY DIFFRACTION99
4.0376-4.34910.28411380.22842714X-RAY DIFFRACTION98
4.3491-4.78630.26261480.22462643X-RAY DIFFRACTION96
4.7863-5.47780.30931350.25612640X-RAY DIFFRACTION95
5.4778-6.89720.3181360.30092672X-RAY DIFFRACTION96
6.8972-44.24590.3091460.30972657X-RAY DIFFRACTION94

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