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- PDB-1mpy: STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PS... -

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Basic information

Entry
Database: PDB / ID: 1mpy
TitleSTRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2
ComponentsCATECHOL 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / CATECHOL 2 / 3-DIOXYGENASE / EXTRADIOL DIOXYGENASE / NON HEME IRON DIOXYGENASE / METAPYROCATECHASE
Function / homology
Function and homology information


catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / toluene catabolic process / ferrous iron binding
Similarity search - Function
: / Catechol 2,3 dioxygenase / Catechol 2,3-dioxygenase-like N-terminal domain / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / : / 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 ...: / Catechol 2,3 dioxygenase / Catechol 2,3-dioxygenase-like N-terminal domain / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / : / 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
ACETONE / : / Metapyrocatechase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsKita, A. / Kita, S. / Fujisawa, I. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2.
Authors: Kita, A. / Kita, S. / Fujisawa, I. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K.
#1: Journal: J.Biochem.(Tokyo) / Year: 1997
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Expressed Pseudomonas Putida Catechol 2,3-Dioxygenase
Authors: Kita, A. / Kita, S. / Inaka, K. / Ishida, T. / Horiike, K. / Nozaki, M. / Miki, K.
History
DepositionOct 20, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27112
Polymers140,8154
Non-polymers4568
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14790 Å2
ΔGint-92 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.000, 264.000, 59.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.90005, 0.43032, -0.06877), (0.42949, 0.84923, -0.30717), (-0.07378, -0.30601, -0.94917)128.85001, -29.71, 1.29
2given(0.89947, -0.43696, 0.00415), (-0.43694, -0.89948, -0.00434), (0.00563, 0.00209, -0.99998)13.25, 57.57, -8.85
3given(-0.99792, 0.01238, 0.06329), (0.00793, -0.95039, 0.31096), (0.064, 0.31081, 0.94832)142.27, 27.88, -9.12

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Components

#1: Protein
CATECHOL 2,3-DIOXYGENASE / METAPYROCATECHASE / MPC


Mass: 35203.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: FE(II) FORM / Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: MT-2 / Gene: XYLE / Plasmid: PHT3 / Species (production host): Escherichia coli / Gene (production host): XYLE
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P06622, catechol 2,3-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-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE 309S ARE ACETONE MOLECULES ASSIGNED TO THE APPROPRIATE DENSITY FEATURES. ACETONE IS ...RESIDUE 309S ARE ACETONE MOLECULES ASSIGNED TO THE APPROPRIATE DENSITY FEATURES. ACETONE IS INCLUDED AT 10% IN ALL CRYSTAL GROWTH AND STABILIZING SOLUTIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: Kita, A., (1997) J.Biochem.(Tokyo), 122, 201.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)sodium citrate1drop
220 mg/mlprotein1drop
326-30 %(w/v)precipitant1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: FILM
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 46225 / % possible obs: 86 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
DENZOdata reduction
WEISdata scaling
PROTEINdata scaling
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.28 2171 5 %
Rwork0.2 --
obs0.2 43306 84 %
Displacement parametersBiso mean: 14.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9912 0 20 112 10044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.97
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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