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- PDB-5zsz: Catechol 2,3-dioxygenase (C23O64) from Diaphorobacter sp DS2 -

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Basic information

Entry
Database: PDB / ID: 5zsz
TitleCatechol 2,3-dioxygenase (C23O64) from Diaphorobacter sp DS2
ComponentsCatechol 2,3-dioxygenase, Extradiol ring cleavage protein
KeywordsOXIDOREDUCTASE / Apo crystal of catechol 2 / 3 dioxygenase
Function / homology
Function and homology information


catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / catabolic process / ferrous iron binding
Similarity search - Function
Catechol 2,3 dioxygenase / Catechol 2,3-dioxygenase-like N-terminal domain / 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 ...Catechol 2,3 dioxygenase / Catechol 2,3-dioxygenase-like N-terminal domain / 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
: / Metapyrocatechase
Similarity search - Component
Biological speciesDiaphorobacter sp. DS2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMishra, K. / Arya, C.K. / Subramanian, R. / Ramanathan, G.
Funding support India, 5items
OrganizationGrant numberCountry
BT/IN/SWEDEN/41/SR/2013 India
BT/PR5081/INF/156/2012 India
BT/PR12422/MED/31/287/214 India
BT/INF/22/SP22660/2017 India
09/092(0869)/2013-EMR-I India
CitationJournal: To Be Published
Title: Catechol 2,3-dioxygenase (C23O64) from Diaphorobacter sp DS2
Authors: Mishra, K. / Arya, C.K. / Subramanian, R. / Ramanathan, G.
History
DepositionApr 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol 2,3-dioxygenase, Extradiol ring cleavage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6513
Polymers32,5551
Non-polymers962
Water45025
1
A: Catechol 2,3-dioxygenase, Extradiol ring cleavage protein
hetero molecules

A: Catechol 2,3-dioxygenase, Extradiol ring cleavage protein
hetero molecules

A: Catechol 2,3-dioxygenase, Extradiol ring cleavage protein
hetero molecules

A: Catechol 2,3-dioxygenase, Extradiol ring cleavage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,60312
Polymers130,2204
Non-polymers3848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area11440 Å2
ΔGint-171 kcal/mol
Surface area41680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.454, 102.454, 113.348
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Catechol 2,3-dioxygenase, Extradiol ring cleavage protein


Mass: 32554.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diaphorobacter sp. DS2 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A509GUM5*PLUS, catechol 2,3-dioxygenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 291.4 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% v/v PEG, 0.1M HEPES sodium salt pH 7.5, 0.2M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0053 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2018
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0053 Å / Relative weight: 1
ReflectionResolution: 2.4→47.762 Å / Num. obs: 14321 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 49.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.026 / Rrim(I) all: 0.107 / Net I/σ(I): 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.4916.61.14114670.8420.2871.177100
8.98-47.7612.70.0543410.9990.0150.05699.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.762 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2406 706 4.94 %
Rwork0.1996 --
obs0.2017 14284 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.65 Å2 / Biso mean: 56.8712 Å2 / Biso min: 26.74 Å2
Refinement stepCycle: final / Resolution: 2.4→47.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 2 25 2312
Biso mean--72.86 51.64 -
Num. residues----293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4001-2.58540.35551480.27062623
2.5854-2.84560.29971270.23542679
2.8456-3.25730.29161410.22822667
3.2573-4.10350.24051410.18632727
Refinement TLS params.Method: refined / Origin x: 30.1932 Å / Origin y: 12.8328 Å / Origin z: 48.2685 Å
111213212223313233
T0.263 Å20.0736 Å20.0241 Å2-0.4743 Å20.091 Å2--0.3346 Å2
L0.7889 °20.2835 °2-0.0742 °2-1.5456 °20.1476 °2--2.1457 °2
S0.0678 Å °0.1361 Å °0.0545 Å °-0.1631 Å °0.0276 Å °-0.0803 Å °-0.3225 Å °-0.063 Å °-0.0926 Å °
Refinement TLS groupSelection details: all

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