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- PDB-3i4y: Crystal structure determination of Catechol 1,2-Dioxygenase from ... -

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Basic information

Entry
Database: PDB / ID: 3i4y
TitleCrystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatechol
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
3,5-dichlorobenzene-1,2-diol / Chem-6PL / : / Catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionJul 3, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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)30,7324
Polymers29,7341
Non-polymers9983
Water4,125229
1
A: Catechol 1,2-dioxygenase
hetero molecules

A: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4648
Polymers59,4682
Non-polymers1,9966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8610 Å2
ΔGint-65 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.818, 37.619, 74.817
Angle α, β, γ (deg.)90.00, 94.81, 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: 29734.037 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-35C / 3,5-dichlorobenzene-1,2-diol


Mass: 179.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4Cl2O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400 38%, MGCL2 0.1 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.0028 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0028 Å / Relative weight: 1
ReflectionResolution: 1.85→74.7 Å / Num. all: 21143 / Num. obs: 21143 / % possible obs: 96.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2943 / Rsym value: 0.539 / % possible all: 93.4

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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: 1.85→74.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.669 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26712 1081 5.1 %RANDOM
Rwork0.20384 ---
obs0.20705 20060 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20.02 Å2
2--0.61 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 52 229 2283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222121
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9692886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88825.05297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96815315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.997158
X-RAY DIFFRACTIONr_chiral_restr0.1420.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021646
X-RAY DIFFRACTIONr_nbd_refined0.2380.21056
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2168
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.231
X-RAY DIFFRACTIONr_mcbond_it1.0571.51314
X-RAY DIFFRACTIONr_mcangle_it1.69522067
X-RAY DIFFRACTIONr_scbond_it2.4583952
X-RAY DIFFRACTIONr_scangle_it3.5844.5818
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 79 -
Rwork0.289 1406 -
obs--92.06 %

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