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- PDB-1cjx: CRYSTAL STRUCTURE OF PSEUDOMONAS FLUORESCENS HPPD -

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Basic information

Entry
Database: PDB / ID: 1cjx
TitleCRYSTAL STRUCTURE OF PSEUDOMONAS FLUORESCENS HPPD
Components4-HYDROXYPHENYLPYRUVATE DIOXYGENASE
KeywordsOXIDOREDUCTASE / Dioxygenase / Iron
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / metal ion binding
Similarity search - Function
Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal / 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. ...Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal / 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 / ETHYL MERCURY ION / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsSerre, L. / Sailland, A. / Sy, D. / Boudec, P. / Rolland, A. / Pebay-Peroulla, E. / Cohen-Addad, C.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of Pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: an enzyme involved in the tyrosine degradation pathway.
Authors: Serre, L. / Sailland, A. / Sy, D. / Boudec, P. / Rolland, A. / Pebay-Peyroula, E. / Cohen-Addad, C.
History
DepositionApr 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)161,75616
Polymers160,3784
Non-polymers1,37812
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-88 kcal/mol
Surface area56370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.590, 142.750, 159.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99838, 9.0E-5, 0.05688), (-0.00585, 0.99487, -0.10101), (0.05658, -0.10118, 0.99326)11.86107, 82.60236, 3.76406
2given(0.41602, 0.90933, -0.00674), (0.90928, -0.41607, -0.00997), (-0.01187, -0.00198, -0.99993)-31.37813, 49.91227, 83.42739
3given(-0.40562, -0.91264, -0.05067), (-0.91182, 0.40015, 0.09198), (-0.06367, 0.08351, -0.99447)47.88144, 25.75212, 80.30645

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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) / Cell line: A32 / Cell line (production host): A32 / Production host: Pseudomonas fluorescens (bacteria)
References: UniProt: P80064, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#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.: 567 / 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: 2.83 Å3/Da / Density % sol: 57.2 %
Crystal growpH: 5.6
Details: 18-25 % PEG 4000 0.2 M AMMONIUM ACETATE, 0.1 M CITRATE, PH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-25 %PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 Mtrisodium citrate1reservoir
410-13 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.91
DetectorDetector: CCD / Date: Jun 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 64393 / % possible obs: 93.2 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rsym value: 8 / Net I/σ(I): 41.67
Reflection shellResolution: 2.4→3 Å / Redundancy: 3.1 % / Rsym value: 14.3 / % possible all: 86.7
Reflection
*PLUS
Num. measured all: 283368 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→20 Å / SU B: 9.01 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3153 5 %RANDOM
Rwork0.219 ---
obs-62863 79.8 %-
Displacement parametersBiso mean: 31.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11222 0 32 567 11821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.853
X-RAY DIFFRACTIONp_mcangle_it2.8455
X-RAY DIFFRACTIONp_scbond_it4.7196
X-RAY DIFFRACTIONp_scangle_it6.0398
X-RAY DIFFRACTIONp_plane_restr0.0254
X-RAY DIFFRACTIONp_chiral_restr0.1080.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.130.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor17.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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