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

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Basic information

Entry
Database: PDB / ID: 3hkp
TitleCrystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate
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 / 3,4-DIHYDROXYBENZOIC ACID / : / 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
DepositionMay 25, 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 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)31,7004
Polymers30,7271
Non-polymers9733
Water3,909217
1
A: Catechol 1,2-dioxygenase
hetero molecules

A: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4008
Polymers61,4542
Non-polymers1,9466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9560 Å2
ΔGint-89 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.420, 37.390, 74.100
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 30727.029 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-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#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.: 217 / 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: 1.98 Å3/Da / Density % sol: 37.92 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.992 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.85→73.72 Å / Num. obs: 20872 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3014 / Rsym value: 0.458 / % possible all: 100

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Processing

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

3hgi


Resolution: 1.85→34.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.771 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25825 1063 5.1 %RANDOM
Rwork0.19403 ---
obs0.19725 19646 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20.49 Å2
2--0.71 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 53 217 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222126
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9662893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81125.10298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39115323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.956158
X-RAY DIFFRACTIONr_chiral_restr0.1480.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021647
X-RAY DIFFRACTIONr_nbd_refined0.2250.21080
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2181
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.239
X-RAY DIFFRACTIONr_mcbond_it1.0811.51324
X-RAY DIFFRACTIONr_mcangle_it1.69622080
X-RAY DIFFRACTIONr_scbond_it2.6953930
X-RAY DIFFRACTIONr_scangle_it4.0644.5811
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 85 -
Rwork0.303 1402 -
obs--97.64 %

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