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- PDB-5zsx: Catechol 2,3-dioxygenase with 3-fluorocatechol from Diaphorobacte... -

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Basic information

Entry
Database: PDB / ID: 5zsx
TitleCatechol 2,3-dioxygenase with 3-fluorocatechol from Diaphorobacter sp DS2
ComponentsCatechol 2,3-dioxygenase, extradiol protein
KeywordsOXIDOREDUCTASE / Crystal of catechol 2 / 3 dioxygenase soaked in 3-fluorocatechol
Function / homology
Function and homology information


catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / aromatic compound catabolic process / 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
3-FLUOROBENZENE-1,2-DIOL / : / DI(HYDROXYETHYL)ETHER / Metapyrocatechase
Similarity search - Component
Biological speciesDiaphorobacter sp. DS2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 with 3-fluorocatechol from Diaphorobacter sp DS2.
Authors: Mishra, K. / Arya, C.K. / Subramanian, R. / Ramanathan, G.
History
DepositionApr 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 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_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.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.value / _struct_conn.pdbx_dist_value / _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

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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)35,3747
Polymers34,9191
Non-polymers4546
Water1,15364
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)141,49528
Polymers139,6784
Non-polymers1,81724
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 area15940 Å2
ΔGint-145 kcal/mol
Surface area41880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.281, 102.281, 113.851
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) / Strain: DS2
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, 70 molecules

#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 / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-3FA / 3-FLUOROBENZENE-1,2-DIOL / 3-FLUOROCATECHOL


Mass: 128.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5FO2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.46 Å3/Da / Density % sol: 50.03 % / 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 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: 2.2→47.89 Å / Num. obs: 18464 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 40.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Net I/σ(I): 32.5 / Num. measured all: 234220 / Scaling rejects: 68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2712.61.04215660.9470.3061.087100
9.07-47.8910.10.02132710.0070.02299.4

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.2→47.889 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 932 5.11 %
Rwork0.1866 17311 -
obs0.1892 18243 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.83 Å2 / Biso mean: 49.4866 Å2 / Biso min: 26.01 Å2
Refinement stepCycle: final / Resolution: 2.2→47.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 26 64 2544
Biso mean--60.44 46.77 -
Num. residues----314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.3160.41681320.38692248238092
2.316-2.46110.31131190.230824532572100
2.4611-2.65120.29651240.208724522576100
2.6512-2.91790.23911240.19324812605100
2.9179-3.34010.25581250.18224942619100
3.3401-4.20770.21430.154825132656100
4.2077-47.90010.21211650.171926702835100
Refinement TLS params.Method: refined / Origin x: 30.8923 Å / Origin y: 13.5575 Å / Origin z: 49.2632 Å
111213212223313233
T0.2481 Å20.0441 Å20.0417 Å2-0.4524 Å20.0882 Å2--0.3243 Å2
L1.2242 °2-0.0041 °20.0075 °2-1.316 °20.3058 °2--2.3219 °2
S0.0999 Å °0.1221 Å °0.145 Å °-0.1068 Å °-0.006 Å °-0.0973 Å °-0.3257 Å °0.0695 Å °-0.0926 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:314)

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