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- PDB-3hjq: Crystal structure of catechol 1,2-dioxygenase from Rhodococcus op... -

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Basic information

Entry
Database: PDB / ID: 3hjq
TitleCrystal structure of catechol 1,2-dioxygenase from Rhodococcus opacus 1CP in complex with 3-methylcatechol
ComponentsCatechol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / BETA-SANDWICH / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Metal-binding
Function / homology
Function and homology information


catechol-containing compound metabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / catabolic process / ferric iron binding
Similarity search - Function
Catechol 1,2-dioxygenase multimerisation domain-like / Catechol 1,2-dioxygenase, actinobacteria / Catechol 1,2-dioxygenase multimerisation domain / Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Helicase, Ruva Protein; domain 3 / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. ...Catechol 1,2-dioxygenase multimerisation domain-like / Catechol 1,2-dioxygenase, actinobacteria / Catechol 1,2-dioxygenase multimerisation domain / Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Helicase, Ruva Protein; domain 3 / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase / Helix non-globular / Special / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6PL / : / 3-METHYLCATECHOL / Catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMatera, I. / Ferraroni, M. / Briganti, F. / Scozzafava, A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts.
Authors: Matera, I. / Ferraroni, M. / Kolomytseva, M. / Golovleva, L. / Scozzafava, A. / Briganti, F.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6684
Polymers30,7251
Non-polymers9433
Water1,62190
1
A: Catechol 1,2-dioxygenase
hetero molecules

A: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3368
Polymers61,4502
Non-polymers1,8866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9500 Å2
ΔGint-102 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.938, 37.585, 74.810
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-291-

HOH

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Components

#1: Protein Catechol 1,2-dioxygenase / 1 / 2-CTD


Mass: 30725.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: grown on benzoate / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP / References: UniProt: P95607, catechol 1,2-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-6PL / (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 763.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-MBD / 3-METHYLCATECHOL / 3-METHYL-BENZENE-1,2-DIOL


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE MATCHES THE GENBANK DEPOSITION WITH ACCESSION CODE CAA67941, IN WHICH ALL 280 RESIDUES ...THE SEQUENCE MATCHES THE GENBANK DEPOSITION WITH ACCESSION CODE CAA67941, IN WHICH ALL 280 RESIDUES ARE PRESENT.

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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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 39% PEG 400, 0.1 M Hepes, 0.1 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.77 Å / Num. obs: 15870 / % possible obs: 94 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 10
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2208 / Rsym value: 0.515 / % possible all: 90.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0044refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3HGI

3hgi


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.164 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27349 813 5.1 %RANDOM
Rwork0.22685 ---
obs0.22936 15046 93.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.939 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å21.41 Å2
2---0.45 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 51 90 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222111
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9652870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5825.05297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.881158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211631
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.51276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48322065
X-RAY DIFFRACTIONr_scbond_it2.4883835
X-RAY DIFFRACTIONr_scangle_it3.7724.5805
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 53 -
Rwork0.313 1053 -
obs--91.1 %

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