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- PDB-2azq: Crystal Structure of Catechol 1,2-Dioxygenase from Pseudomonas ar... -

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Basic information

Entry
Database: PDB / ID: 2azq
TitleCrystal Structure of Catechol 1,2-Dioxygenase from Pseudomonas arvilla C-1
Componentscatechol 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / CTD / Catechol / Dioxygenase / lipid / isozyme / intradiol
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
: / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsEarhart, C.A. / Vetting, M.W. / Gosu, R. / Michaud-Soret, I. / Que, L. / Ohlendorf, D.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Structure of catechol 1,2-dioxygenase from Pseudomonas arvilla
Authors: Earhart, C.A. / Vetting, M.W. / Gosu, R. / Michaud-Soret, I. / Que, L. / Ohlendorf, D.H.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _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)35,1443
Polymers34,3541
Non-polymers7902
Water00
1
A: catechol 1,2-dioxygenase
hetero molecules

A: catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2886
Polymers68,7082
Non-polymers1,5804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9730 Å2
ΔGint-119 kcal/mol
Surface area27750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.73, 71.52, 187.09
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is dimer. It is generated by 2fold rotation about x axis: x,-y,-z

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Components

#1: Protein catechol 1,2-dioxygenase / E.C.1.13.11.1


Mass: 34354.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: synonym Pseudomonas arvilla / Source: (natural) Pseudomonas putida (bacteria) / Strain: C-1 / References: UniProt: Q51433, 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-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P

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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: 3.05 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.6
Details: Tris/Malate, PEG 8000, Magnesium acetate, pH 7.6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: Copper K-alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→21 Å / Num. obs: 25259 / % possible obs: 84.4 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 30 Å2 / Net I/σ(I): 9.9

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLT

1dlt


Resolution: 2.65→21 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 555 4.4 %random
Rwork0.229 ---
all0.267 10566 --
obs0.238 10566 84.4 %-
Solvent computationBsol: 16.542 Å2
Displacement parametersBiso mean: 15.597 Å2
Baniso -1Baniso -2Baniso -3
1--1.875 Å20 Å20 Å2
2--1.367 Å20 Å2
3---0.508 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: LAST / Resolution: 2.65→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 45 0 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_mcbond_it1.4531.5
X-RAY DIFFRACTIONc_mcangle_it2.4582
X-RAY DIFFRACTIONc_scbond_it2.2452
X-RAY DIFFRACTIONc_scangle_it3.6052.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4lip_even_prodrg2.param

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