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- PDB-3hhy: Crystal structure determination of Catechol 1,2-Dioxygenase from ... -

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Basic information

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


chlorocatechol 1,2-dioxygenase activity / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / catechol-containing compound metabolic 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 / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase ...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 / Intradiol ring-cleavage dioxygenases signature. / Protocatechuate 3,4-Dioxygenase, subunit A / Aromatic compound dioxygenase / 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 / CATECHOL / : / Catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMatera, I. / Ferraroni, M. / Kolomytseva, 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 18, 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,00510
Polymers30,7251
Non-polymers1,2809
Water5,170287
1
A: Catechol 1,2-dioxygenase
hetero molecules

A: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,01020
Polymers61,4502
Non-polymers2,56018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11160 Å2
ΔGint-124 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.829, 37.482, 74.479
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-443-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 30725.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP / References: UniProt: P95607, catechol 1,2-dioxygenase

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Non-polymers , 6 types, 296 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE / Catechol


Mass: 110.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O2
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 39% PEG400, 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: May 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→44.324 Å / Num. obs: 33822 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.215 Å2 / Rsym value: 0.074 / Net I/σ(I): 11.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 14728 / Rsym value: 0.551 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HGI

3hgi


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.324 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1779 5 %RANDOM
Rwork0.20846 ---
obs0.21008 33822 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20.51 Å2
2---0.07 Å20 Å2
3----0.73 Å2
Refine analyzeLuzzati sigma a obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 70 287 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222139
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9712912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1325.10298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65715319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.892158
X-RAY DIFFRACTIONr_chiral_restr0.1270.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021662
X-RAY DIFFRACTIONr_nbd_refined0.2140.21029
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2217
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.244
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0510.21
X-RAY DIFFRACTIONr_mcbond_it0.9671.51312
X-RAY DIFFRACTIONr_mcangle_it1.53622084
X-RAY DIFFRACTIONr_scbond_it2.263944
X-RAY DIFFRACTIONr_scangle_it3.2694.5825
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 112 -
Rwork0.291 2447 -
obs--98.42 %

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