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- PDB-5znh: Catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobact... -

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Basic information

Entry
Database: PDB / ID: 5znh
TitleCatechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2
ComponentsCatechol 2,3-dioxygenase, extradiol protein
KeywordsOXIDOREDUCTASE / complex with 4-methylcatechol
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
: / 4-METHYLCATECHOL / DI(HYDROXYETHYL)ETHER / Metapyrocatechase
Similarity search - Component
Biological speciesDiaphorobacter sp. DS2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMishra, K. / Arya, C.K. / Subramaniyan, 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 with 4-methyl catechol from Diaphorobacter sp DS2
Authors: Mishra, K. / Arya, C.K. / Subramaniyan, R. / Ramanathan, G.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3086
Polymers34,9191
Non-polymers3885
Water59433
1
A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules

A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules

A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules

A: Catechol 2,3-dioxygenase, extradiol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,23124
Polymers139,6784
Non-polymers1,55320
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 area15550 Å2
ΔGint-167 kcal/mol
Surface area41380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.894, 101.894, 114.369
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol 2,3-dioxygenase, extradiol protein


Mass: 34919.488 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: A0A4V8GZK8*PLUS, catechol 2,3-dioxygenase

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Non-polymers , 6 types, 38 molecules

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


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


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.45 Å3/Da / Density % sol: 49.88 % / Description: Diamond shaped crystal
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→47.99 Å / Num. obs: 14302 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 45.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Net I/σ(I): 22.4 / Num. measured all: 145849 / Scaling rejects: 155
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4910.60.6741548614670.8970.2150.7093.7100
8.98-47.9980.03727433430.9990.0120.03952.699.5

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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
Starting model: 3HQ0

3hq0


Resolution: 2.4→47.989 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 716 5.02 %
Rwork0.1988 13539 -
obs0.2009 14255 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.48 Å2 / Biso mean: 53.5438 Å2 / Biso min: 27.03 Å2
Refinement stepCycle: final / Resolution: 2.4→47.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 22 33 2509
Biso mean--55.96 47.38 -
Num. residues----314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4001-2.58540.33251340.242526372771
2.5854-2.84560.26381330.231826712804
2.8456-3.25730.28771490.223226572806
3.2573-4.10350.21261470.192726922839
4.1035-47.99860.22051530.179228823035
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)
12.38810.23290.21751.9877-0.20631.53770.30190.70890.2743-0.3698-0.19090.0788-0.20730.101-0.110.35230.25170.09050.79030.11690.421732.837112.435937.2124
22.8432-0.02030.63831.618-0.5251.16870.3590.44760.2109-0.2031-0.17910.4659-0.3048-0.4515-0.14340.31140.25550.00120.75040.02960.507314.491411.878943.9086
31.93030.23220.28062.23930.2261.03860.35520.3590.2202-0.198-0.27240.1712-0.1427-0.1251-0.12610.29470.19460.0580.6383-0.01060.351728.704210.459646.4032
41.71010.06760.00251.1893-0.50921.52190.3064-0.10450.24490.101-0.24590.1491-0.2039-0.0127-0.09590.30820.03780.11660.5315-0.06080.463531.003814.815756.7653
52.13810.12120.42031.6256-0.60531.71220.3897-0.27980.64770.0655-0.6125-0.0831-0.18390.6179-0.09460.35780.06990.17280.68280.04850.583642.683216.101451.5949
61.9135-0.48630.64411.6396-0.56691.6290.5557-0.26560.58420.1597-0.6239-0.5266-0.51430.4179-0.04290.4111-0.11170.16170.642-0.07050.553536.329516.96263.4269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )A1 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 103 )A63 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 164 )A104 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 240 )A165 - 240
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 274 )A241 - 274
6X-RAY DIFFRACTION6chain 'A' and (resid 275 through 314 )A275 - 314

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