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- PDB-3hpy: Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseud... -

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Basic information

Entry
Database: PDB / ID: 3hpy
TitleCrystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in the complex with 4-methylcatechol
ComponentsCatechol 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / repeated motifs / Aromatic hydrocarbons catabolism / Dioxygenase / Iron
Function / homology
Function and homology information


catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / : / ferrous iron binding
Similarity search - Function
Catechol 2,3 dioxygenase / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase ...Catechol 2,3 dioxygenase / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / 4-METHYLCATECHOL / Metapyrocatechase
Similarity search - Component
Biological speciesPseudomonas sp. KL28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.94 Å
AuthorsCho, J.-H. / Rhee, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas
Authors: Cho, J.-H. / Jung, D.-K. / Lee, K. / Rhee, S.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catechol 2,3-dioxygenase
B: Catechol 2,3-dioxygenase
C: Catechol 2,3-dioxygenase
D: Catechol 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,08611
Polymers140,4904
Non-polymers5967
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-97 kcal/mol
Surface area39510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.100, 97.600, 133.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Catechol 2,3-dioxygenase /


Mass: 35122.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. KL28 (bacteria) / Strain: KCTC 22206 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7WYF5, catechol 2,3-dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MCT / 4-METHYLCATECHOL / 4-METHYL-1,2-BENZENEDIOL / 4-Methylcatechol


Mass: 124.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.23 Å3/Da / Density % sol: 44.88 % / Mosaicity: 0.771 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium fluoride, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 28, 2008
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 93774 / Num. obs: 81556 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 11.5 % / Rmerge(I) obs: 0.071 / Χ2: 0.996 / Net I/σ(I): 35.92
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9260 / Χ2: 0.724 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: Native final model

Resolution: 1.94→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: using a random selection of data / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 8169 -RANDOM
Rwork0.244 ---
all-81556 --
obs-73387 78.4 %-
Displacement parametersBiso max: 66.51 Å2 / Biso mean: 30.394 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.852 Å20 Å20 Å2
2--0.155 Å20 Å2
3---0.697 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9324 0 31 351 9706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012134
X-RAY DIFFRACTIONc_angle_deg1.88504
LS refinement shellResolution: 1.94→2.01 Å

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