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- PDB-7x8e: Crystal structure of PfHPPD-Y13287 complex -

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Basic information

Entry
Database: PDB / ID: 7x8e
TitleCrystal structure of PfHPPD-Y13287 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / complex / substrate
Function / homology
Function and homology information


aromatic amino acid metabolic process / 4-hydroxyphenylpyruvate dioxygenase activity / metal ion binding
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
Chem-92X / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.749 Å
AuthorsDong, J. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Agrochem / Year: 2022
Title: Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules
Authors: Dong, J. / Dong, J. / Yu, X.H. / Yan, Y.C. / Nan, J.X. / He, B. / Ye, B.Q. / Yang, W.C. / Lin, H.Y. / Yang, G.F.
History
DepositionMar 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
E: 4-hydroxyphenylpyruvate dioxygenase
F: 4-hydroxyphenylpyruvate dioxygenase
G: 4-hydroxyphenylpyruvate dioxygenase
H: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,57424
Polymers320,7558
Non-polymers3,81916
Water3,135174
1
A: 4-hydroxyphenylpyruvate dioxygenase
E: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
E: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,28712
Polymers160,3784
Non-polymers1,9108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5640 Å2
ΔGint-20 kcal/mol
Surface area55350 Å2
MethodPISA
2
B: 4-hydroxyphenylpyruvate dioxygenase
C: 4-hydroxyphenylpyruvate dioxygenase
F: 4-hydroxyphenylpyruvate dioxygenase
H: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,28712
Polymers160,3784
Non-polymers1,9108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-18 kcal/mol
Surface area54280 Å2
MethodPISA
3
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

G: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

G: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,28712
Polymers160,3784
Non-polymers1,9108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_456-x-1/2,y+1/2,-z+11
Buried area5870 Å2
ΔGint-17 kcal/mol
Surface area53710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.699, 161.203, 121.984
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
4-hydroxyphenylpyruvate dioxygenase


Mass: 40094.422 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: ALQ17_04098, AO066_02200
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0W0HIR1
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-92X / 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 418.442 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H22N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES 6.5, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.749→50 Å / Num. obs: 79289 / % possible obs: 98.7 % / Redundancy: 3.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.8
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 3889 / CC1/2: 0.835 / % possible all: 97.5

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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: 1CJX

1cjx


Resolution: 2.749→38.154 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 3831 4.84 %
Rwork0.1963 --
obs0.2 79161 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.749→38.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21106 0 256 174 21536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921879
X-RAY DIFFRACTIONf_angle_d1.04129592
X-RAY DIFFRACTIONf_dihedral_angle_d6.74913483
X-RAY DIFFRACTIONf_chiral_restr0.0553078
X-RAY DIFFRACTIONf_plane_restr0.0063904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7492-2.78390.391740.29672394X-RAY DIFFRACTION86
2.7839-2.82060.38181760.27722709X-RAY DIFFRACTION97
2.8206-2.85920.34981540.26952777X-RAY DIFFRACTION99
2.8592-2.90.30741190.23212827X-RAY DIFFRACTION100
2.9-2.94330.2871510.2192789X-RAY DIFFRACTION100
2.9433-2.98930.31581740.22272835X-RAY DIFFRACTION99
2.9893-3.03830.3441200.22652850X-RAY DIFFRACTION99
3.0383-3.09060.33861560.24762786X-RAY DIFFRACTION99
3.0906-3.14680.31181530.24352833X-RAY DIFFRACTION99
3.1468-3.20730.34271170.22682842X-RAY DIFFRACTION99
3.2073-3.27270.3991360.22782793X-RAY DIFFRACTION99
3.2727-3.34390.36751420.23172771X-RAY DIFFRACTION99
3.3439-3.42160.32011540.21872813X-RAY DIFFRACTION99
3.4216-3.50710.30331570.21752727X-RAY DIFFRACTION98
3.5071-3.60190.2641650.21032783X-RAY DIFFRACTION99
3.6019-3.70780.29231300.20312799X-RAY DIFFRACTION97
3.7078-3.82730.30551500.19192797X-RAY DIFFRACTION99
3.8273-3.9640.25051350.18782871X-RAY DIFFRACTION100
3.964-4.12250.26881120.18692798X-RAY DIFFRACTION99
4.1225-4.30990.27991310.1752832X-RAY DIFFRACTION99
4.3099-4.53680.22411470.16962816X-RAY DIFFRACTION99
4.5368-4.82050.2141210.15752793X-RAY DIFFRACTION98
4.8205-5.19190.22191590.16482827X-RAY DIFFRACTION98
5.1919-5.71280.21341240.17372783X-RAY DIFFRACTION98
5.7128-6.53590.28931960.18512802X-RAY DIFFRACTION100
6.5359-8.22090.25331000.17692902X-RAY DIFFRACTION99
8.2209-38.1540.189780.1842781X-RAY DIFFRACTION93

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