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- PDB-7xnt: Crystal structure of PfHPPD-Y13161 complex -

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Basic information

Entry
Database: PDB / ID: 7xnt
TitleCrystal structure of PfHPPD-Y13161 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / Complex
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-94L / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.822 Å
AuthorsLin, 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
DepositionApr 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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
G: 4-hydroxyphenylpyruvate dioxygenase
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
C: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,28712
Polymers160,3784
Non-polymers1,9108
Water6,936385
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.943, 73.041, 87.963
Angle α, β, γ (deg.)66.13, 79.56, 69.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
4-hydroxyphenylpyruvate dioxygenase


Mass: 40094.422 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-94L / 3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 418.442 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C24H22N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 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: 1.82→50 Å / Num. obs: 130085 / % possible obs: 97.9 % / Redundancy: 3.47 % / CC1/2: 0.9795 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11.4
Reflection shellResolution: 1.82→1.87 Å / Rmerge(I) obs: 1.356 / Num. unique obs: 9505 / CC1/2: 0.277

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X8E

7x8e


Resolution: 1.822→34.897 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 6499 5 %
Rwork0.2377 --
obs0.2394 130007 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.822→34.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10319 0 128 385 10832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910745
X-RAY DIFFRACTIONf_angle_d1.05514547
X-RAY DIFFRACTIONf_dihedral_angle_d5.7666280
X-RAY DIFFRACTIONf_chiral_restr0.0571524
X-RAY DIFFRACTIONf_plane_restr0.0071908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.822-1.84220.41672250.38524062X-RAY DIFFRACTION96
1.8422-1.86390.39622370.37683992X-RAY DIFFRACTION96
1.8639-1.88660.36971980.36984134X-RAY DIFFRACTION97
1.8866-1.91050.38762110.34964018X-RAY DIFFRACTION97
1.9105-1.93570.35362490.34354073X-RAY DIFFRACTION97
1.9357-1.96220.37122300.33274045X-RAY DIFFRACTION97
1.9622-1.99020.37382150.3334076X-RAY DIFFRACTION97
1.9902-2.01990.38872200.31264085X-RAY DIFFRACTION97
2.0199-2.05150.32681880.30594092X-RAY DIFFRACTION97
2.0515-2.08510.33362090.29944139X-RAY DIFFRACTION97
2.0851-2.1210.32742160.29764098X-RAY DIFFRACTION97
2.121-2.15960.32671870.2834076X-RAY DIFFRACTION97
2.1596-2.20110.33912340.28114093X-RAY DIFFRACTION97
2.2011-2.24610.33291730.27184138X-RAY DIFFRACTION98
2.2461-2.29490.27942220.2634125X-RAY DIFFRACTION98
2.2949-2.34830.30592030.26034124X-RAY DIFFRACTION98
2.3483-2.4070.30832210.26324133X-RAY DIFFRACTION98
2.407-2.4720.3282370.27634107X-RAY DIFFRACTION98
2.472-2.54480.32482290.26784131X-RAY DIFFRACTION98
2.5448-2.62690.30332220.27264111X-RAY DIFFRACTION98
2.6269-2.72070.31632300.25974121X-RAY DIFFRACTION98
2.7207-2.82960.29122180.25154167X-RAY DIFFRACTION98
2.8296-2.95830.24432150.24584135X-RAY DIFFRACTION99
2.9583-3.11420.30082140.24014161X-RAY DIFFRACTION99
3.1142-3.30920.25912120.24454184X-RAY DIFFRACTION99
3.3092-3.56440.27271940.22744171X-RAY DIFFRACTION99
3.5644-3.92270.25061910.20934225X-RAY DIFFRACTION99
3.9227-4.48930.21112380.18864151X-RAY DIFFRACTION99
4.4893-5.65220.21732360.18644178X-RAY DIFFRACTION99
5.6522-34.8970.23422250.21064163X-RAY DIFFRACTION99

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