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- PDB-6j63: Crystal structure of Arabidopsis thaliana HPPD complexed with NTBC -

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Basic information

Entry
Database: PDB / ID: 6j63
TitleCrystal structure of Arabidopsis thaliana HPPD complexed with NTBC
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / 4-hydroxyphenylpyruvate dioxygenase / nitisinone / type I tyrosinemia / drug discovery
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 / 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
: / Chem-NTD / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.624 Å
AuthorsYang, W.C. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21332004 China
CitationJournal: FEBS J. / Year: 2019
Title: Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations.
Authors: Lin, H.Y. / Yang, J.F. / Wang, D.W. / Hao, G.F. / Dong, J.Q. / Wang, Y.X. / Yang, W.C. / Wu, J.W. / Zhan, C.G. / Yang, G.F.
History
DepositionJan 13, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 6, 2019ID: 5CTO
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)197,03612
Polymers195,4954
Non-polymers1,5408
Water32418
1
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5186
Polymers97,7482
Non-polymers7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-29 kcal/mol
Surface area27910 Å2
MethodPISA
2
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5186
Polymers97,7482
Non-polymers7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-28 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.660, 95.960, 97.930
Angle α, β, γ (deg.)90.00, 92.15, 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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-NTD / 2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE


Mass: 329.228 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10F3NO5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 291.16 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M NaAc at pH 4.5, 0.1M NaCl, 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 52627 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.764 / Rmerge(I) obs: 0.571 / Rsym value: 0.571 / Net I/σ(I): 9.72
Reflection shellResolution: 2.62→2.77 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.687 / Num. unique obs: 7642 / CC1/2: 0.429 / Rsym value: 1.687 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SQD

1sqd


Resolution: 2.624→29.187 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3009 2671 5.08 %
Rwork0.2779 --
obs0.2791 52557 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.624→29.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11057 0 96 18 11171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311404
X-RAY DIFFRACTIONf_angle_d0.61915430
X-RAY DIFFRACTIONf_dihedral_angle_d20.1496644
X-RAY DIFFRACTIONf_chiral_restr0.0461670
X-RAY DIFFRACTIONf_plane_restr0.0052013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.624-2.67170.39571500.37142526X-RAY DIFFRACTION96
2.6717-2.7230.361330.36622630X-RAY DIFFRACTION99
2.723-2.77860.37231380.34432614X-RAY DIFFRACTION100
2.7786-2.8390.36031360.33372660X-RAY DIFFRACTION100
2.839-2.90490.37041230.34172664X-RAY DIFFRACTION100
2.9049-2.97750.36041350.33312646X-RAY DIFFRACTION100
2.9775-3.05790.36131340.33762648X-RAY DIFFRACTION100
3.0579-3.14780.40451340.33322599X-RAY DIFFRACTION100
3.1478-3.24930.35251650.31532624X-RAY DIFFRACTION100
3.2493-3.36530.30791480.27132635X-RAY DIFFRACTION100
3.3653-3.49980.29381450.27892634X-RAY DIFFRACTION100
3.4998-3.65880.29271270.26922670X-RAY DIFFRACTION100
3.6588-3.85130.26151450.25032631X-RAY DIFFRACTION100
3.8513-4.0920.27231250.24172657X-RAY DIFFRACTION100
4.092-4.40690.25351560.22382613X-RAY DIFFRACTION99
4.4069-4.84860.22311420.21292636X-RAY DIFFRACTION99
4.8486-5.5460.2431330.22712649X-RAY DIFFRACTION99
5.546-6.97170.29391650.24872625X-RAY DIFFRACTION98
6.9717-29.1890.24761370.26072525X-RAY DIFFRACTION92

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