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- PDB-1dlm: STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACE... -

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Basic information

Entry
Database: PDB / ID: 1dlm
TitleSTRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA
ComponentsCATECHOL 1,2-DIOXYGENASE
KeywordsOXIDOREDUCTASE / METALLOPROTEIN / DIOXYGENASE / AROMATIC COMPOUND DEGRADATION / MIXED ALPHA HELIX/ BETA STRAND
Function / homology
Function and homology information


catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function
Catechol 1,2-dioxygenase, proteobacteria / 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 ...Catechol 1,2-dioxygenase, proteobacteria / 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
: / Chem-LIO / Catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsVetting, M.W. / Ohlendorf, D.H.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
Authors: Vetting, M.W. / Ohlendorf, D.H.
#1: Journal: J.Bacteriol. / Year: 1988
Title: DNA Sequence of the Acinetobacter calcoaceticus Catechol 1,2-dioxygenase I Structural Gene catA: Evidence for Evolutionary Divergence of Intradiol Dioxygenases by Aquisition of DNA Sequence Repetitions
Authors: Neidle, E.L. / Harnett, C. / Bonitz, S. / Ornston, L.N.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Protocatechuate 3,4-dioxygenase from Psuedomonas aeruginosa at 2.15 A Resolution
Authors: Ohlendorf, D.H. / Orville, A.M. / Lipscomb, J.D.
#3: Journal: Biochemistry / Year: 1997
Title: Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-dioxygenase: Endogenous Fe+3 Ligand Displacement in Response to Substrate Binding.
Authors: Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H.
History
DepositionDec 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: CATECHOL 1,2-DIOXYGENASE
B: CATECHOL 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1546
Polymers68,7682
Non-polymers1,3854
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-105 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 87.600, 84.200
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological Assembly of the molecule is homodimer consisting of subunit A and subunit B related by a non-crystallographic two-fold

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Components

#1: Protein CATECHOL 1,2-DIOXYGENASE / 1 / 2-CTD


Mass: 34384.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07773, catechol 1,2-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-LIO / [1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE


Mass: 636.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H67NO8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-15% Peg5000, 100mM Tris-HCl pH 7.5, 0.2M Mg Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mg/mlprotein1drop
215 %PEG50001reservoir
3200 mMmagnesium acetate1reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→100 Å / Num. all: 51520 / Num. obs: 167535 / % possible obs: 80.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.4
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 1.35 % / Rmerge(I) obs: 0.276 / Num. unique all: 3503 / % possible all: 33.1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 53372 / % possible obs: 89.4 % / Num. measured all: 167535
Reflection shell
*PLUS
% possible obs: 76.2 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
X-GENdata reduction
X-GENdata scaling
RefinementResolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 4386 Random 10% of observed reflections with an I/sigma > 0
Rwork0.196 --
all0.196 51506 -
obs0.196 43086 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 88 183 5085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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