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- PDB-3o5u: Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcu... -

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Basic information

Entry
Database: PDB / ID: 3o5u
TitleCrystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate
ComponentsChlorocatechol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / BETA BARREL
Function / homology
Function and homology information


catechol-containing compound metabolic process / catechol 1,2-dioxygenase activity / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / catabolic process / ferric iron binding
Similarity search - Function
Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / 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 ...Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / : / Chem-MYY / Chlorocatechol 1,2-dioxygenase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFerraroni, M. / Briganti, F. / Kolomitseva, M. / Golovleva, L.
CitationJournal: J. Struct. Biol. / Year: 2013
Title: X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity.
Authors: Ferraroni, M. / Kolomytseva, M. / Scozzafava, A. / Golovleva, L. / Briganti, F.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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.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_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: Chlorocatechol 1,2-dioxygenase
B: Chlorocatechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,03915
Polymers57,9592
Non-polymers2,08013
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-118 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.310, 87.310, 185.921
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chlorocatechol 1,2-dioxygenase


Mass: 28979.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodococcus opacus (bacteria) / Strain: 1CP
References: UniProt: O67987, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen

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Non-polymers , 6 types, 350 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MYY / (2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL PALMITATE


Mass: 620.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H65O8P
#4: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 9
Details: ammonium sulphate, NaCl, TRIS, pH 9.0, vapor diffusion, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2008
RadiationMonochromator: Double crystal Si(111), horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→92.96 Å / Num. all: 33380 / Num. obs: 33380 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 40.53 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.486.10.5041.22953648660.504100
2.48-2.636.20.361.92860446100.36100
2.63-2.816.30.252.62706043180.25100
2.81-3.036.30.1793.92528840240.179100
3.03-3.326.20.1235.42307736990.123100
3.32-3.726.20.0986.62090133560.098100
3.72-4.296.10.0966.51826729720.096100
4.29-5.2560.0986.51510825040.098100
5.25-7.436.10.0787.71188819560.078100
7.43-43.6446.10.05310656510750.05398.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S9A

1s9a


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2041 / WRfactor Rwork: 0.1576 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8697 / SU B: 5.815 / SU ML: 0.139 / SU R Cruickshank DPI: 0.2304 / SU Rfree: 0.1952 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1689 5.1 %RANDOM
Rwork0.1663 ---
obs0.1688 33340 99.99 %-
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 max: 93.89 Å2 / Biso mean: 42.1042 Å2 / Biso min: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 122 337 4521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224311
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9565861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.755514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2523.532201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04415637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1891528
X-RAY DIFFRACTIONr_chiral_restr0.1090.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213346
X-RAY DIFFRACTIONr_mcbond_it0.8981.52569
X-RAY DIFFRACTIONr_mcangle_it1.69524178
X-RAY DIFFRACTIONr_scbond_it2.47431742
X-RAY DIFFRACTIONr_scangle_it4.0234.51681
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 124 -
Rwork0.226 2327 -
all-2451 -
obs--99.92 %

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