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- PDB-3th1: Crystal structure of chlorocatechol 1,2-dioxygenase from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3th1
TitleCrystal structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida
ComponentsChlorocatechol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / Catechol 1 / 2-dioxygenase family / iron binding
Function / homology
Function and homology information


: / catechol 1,2-dioxygenase activity / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / catechol-containing compound metabolic process / : / ferric iron binding
Similarity search - Function
Chlorocatechol 1,2-dioxygenase / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / ACETATE ION / DITHIANE DIOL / : / Chlorocatechol 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsRustiguel, J.K. / Nonato, M.C.
CitationJournal: To be Published
Title: Crystal Structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida
Authors: Rustiguel, J.K. / Barbosa, L.R.S. / Araujo, A.P.U. / Nonato, M.C.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_label_asym_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
C: Chlorocatechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,24815
Polymers87,0743
Non-polymers2,17412
Water30617
1
A: Chlorocatechol 1,2-dioxygenase
hetero molecules

A: Chlorocatechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,09114
Polymers58,0492
Non-polymers2,04112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6150 Å2
ΔGint-74 kcal/mol
Surface area22590 Å2
MethodPISA
2
B: Chlorocatechol 1,2-dioxygenase
hetero molecules

C: Chlorocatechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2028
Polymers58,0492
Non-polymers1,1536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
Buried area7460 Å2
ΔGint-87 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.570, 97.570, 423.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-302-

3PH

21A-302-

3PH

31A-268-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Chlorocatechol 1,2-dioxygenase


Mass: 29024.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: clcA / Plasmid: PTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11451, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen

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Non-polymers , 7 types, 29 molecules

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


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H77O8P
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 14% PEG 8000 and 0.2 M magnesium acetate tetrahydrated, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2010
Details: Vertical collimator mirror and toroidal focusing mirror
RadiationMonochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 3.4→59.83 Å / Num. obs: 17523 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 3.1 / Redundancy: 8.6 % / Rmerge(I) obs: 0.213 / Rsym value: 0.213 / Net I/σ(I): 9.6
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.692 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERwizardphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOY

2boy


Resolution: 3.4→54.178 Å / SU ML: 0.83 / Isotropic thermal model: overall / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2787 1747 10 %
Rwork0.2265 --
obs0.2318 17465 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.41 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3908 Å20 Å20 Å2
2--3.3908 Å2-0 Å2
3----7.2313 Å2
Refinement stepCycle: LAST / Resolution: 3.4→54.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 133 17 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045563
X-RAY DIFFRACTIONf_angle_d0.9987584
X-RAY DIFFRACTIONf_dihedral_angle_d16.2221934
X-RAY DIFFRACTIONf_chiral_restr0.069851
X-RAY DIFFRACTIONf_plane_restr0.004988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.50010.35281410.27771276X-RAY DIFFRACTION100
3.5001-3.6130.28681420.26841272X-RAY DIFFRACTION100
3.613-3.74210.27281410.25031271X-RAY DIFFRACTION100
3.7421-3.89190.30251400.23521258X-RAY DIFFRACTION100
3.8919-4.0690.27131430.22021287X-RAY DIFFRACTION100
4.069-4.28340.28271410.19941271X-RAY DIFFRACTION100
4.2834-4.55170.24961440.20311294X-RAY DIFFRACTION100
4.5517-4.90290.24871450.20091309X-RAY DIFFRACTION100
4.9029-5.39590.27321460.20031310X-RAY DIFFRACTION100
5.3959-6.17580.29681480.23141332X-RAY DIFFRACTION100
6.1758-7.77710.28421510.25361354X-RAY DIFFRACTION100
7.7771-54.18490.2741650.2261484X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25570.4693-0.41562.0315-0.94682.32260.0922-0.23230.00990.2866-0.0755-0.3164-0.06320.16020.04040.4701-0.0392-0.05820.2287-0.00590.22151.4744-2.19073.0835
20.90330.0955-0.25720.8443-0.38941.6055-0.0791-0.15430.06740.0055-0.04050.259-0.1754-0.44550.08570.44260.0898-0.09940.2623-0.07470.243239.4349-18.141520.7848
31.49980.26060.22841.92010.46812.00350.0742-0.0374-0.06630.1839-0.1846-0.2682-0.15040.21350.12670.4954-0.0317-0.08480.1812-0.03210.252649.6051-20.400922.016
42.4859-0.2382-0.52041.47380.52611.2306-0.29690.4488-0.96460.25840.2993-0.0087-0.0141-0.72580.0960.3811-0.2503-0.17870.3815-0.47860.720629.0467-35.3964-11.8434
51.024-0.32750.11740.0926-0.06350.8981-0.14330.7456-0.6571-0.32-0.1309-0.4395-0.0920.13580.02621.0316-0.07440.58710.7909-0.41381.324360.693-40.3672-16.7828
64.4832-2.46510.1965.98854.22384.774-0.32021.1798-1.0213-0.1801-0.50090.35660.1615-0.27210.70110.7609-0.21710.30770.9416-0.35591.154757.9137-30.0228-18.221
70.7125-0.3742-0.81863.41011.50311.2912-0.2178-0.0014-0.7957-0.5622-0.0821-1.0750.24660.52190.19060.78050.07430.21930.4758-0.14130.858355.2874-36.6162-9.8379
81.1868-0.5015-0.17421.35820.33812.4583-0.3768-0.2223-0.5425-0.5775-0.0055-0.6050.0942-0.06790.25250.78740.05810.24530.2595-0.23040.621345.58357.851557.3062
92.14140.81080.47531.6483-0.14090.24390.1094-0.01320.29330.3879-0.59570.93990.4104-0.6810.38930.9897-0.12510.16780.7462-0.35390.929321.685-11.054353.6647
101.70290.58150.2222.3967-1.47932.53160.0895-0.24370.0685-0.0518-0.2380.41520.3136-1.17920.19840.8211-0.20250.22660.9821-0.34561.339316.5968-9.675749.2606
111.96770.53780.27962.72020.67432.2778-0.1879-0.1117-0.5984-0.3344-0.15810.66910.2342-0.42180.43250.944-0.17570.25910.6099-0.23170.99728.17-12.809851.6213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:74)
2X-RAY DIFFRACTION2chain 'A' and (resseq 75:194)
3X-RAY DIFFRACTION3chain 'A' and (resseq 195:246)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:65)
5X-RAY DIFFRACTION5chain 'B' and (resseq 66:117)
6X-RAY DIFFRACTION6chain 'B' and (resseq 118:137)
7X-RAY DIFFRACTION7chain 'B' and (resseq 138:244)
8X-RAY DIFFRACTION8chain 'C' and (resseq 1:54)
9X-RAY DIFFRACTION9chain 'C' and (resseq 55:108)
10X-RAY DIFFRACTION10chain 'C' and (resseq 109:147)
11X-RAY DIFFRACTION11chain 'C' and (resseq 148:246)

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