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- PDB-2wl3: crystal structure of catechol 2,3-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 2wl3
Titlecrystal structure of catechol 2,3-dioxygenase
ComponentsCATECHOL 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / AROMATIC HYDROCARBONS CATABOLISM / AKBC
Function / homology
Function and homology information


: / dioxygenase activity / xenobiotic catabolic process / ferrous iron binding
Similarity search - Function
2,3-dihydroxybiphenyl 1,2-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 ...2,3-dihydroxybiphenyl 1,2-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
: / Catechol 2,3-dioxygenase
Similarity search - Component
Biological speciesRHODOCOCCUS SP. DK17 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCho, H.J. / Kim, K.J. / Kang, B.S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Substrate-Binding Mechanism of a Type I Extradiol Dioxygenase.
Authors: Cho, H.J. / Kim, K. / Sohn, S.Y. / Cho, H.Y. / Kim, K.J. / Kim, M.H. / Kim, D. / Kim, E. / Kang, B.S.
History
DepositionJun 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)138,49714
Polymers137,7734
Non-polymers72410
Water4,522251
1
C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,73024
Polymers275,5478
Non-polymers1,18416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area22840 Å2
ΔGint-190.6 kcal/mol
Surface area77820 Å2
MethodPISA
2
A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,25932
Polymers275,5478
Non-polymers1,71224
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area24460 Å2
ΔGint-226.3 kcal/mol
Surface area80640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.373, 102.373, 142.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
CATECHOL 2,3-DIOXYGENASE /


Mass: 34443.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS SP. DK17 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q6REQ5
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSELENOMETHIONINE (MSE): PARENT-MET
Sequence detailsABOUT 20 RESIDUES AT C-TERMINUS ARE DELETED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 30% PEG 400, 0.1M HEPES PH7.5, 0.2M CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.436
11-H, K, -L20.564
ReflectionResolution: 2.2→50 Å / Num. obs: 74911 / % possible obs: 99.8 % / Observed criterion σ(I): 2.2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.58 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→29.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 16.253 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17816 3650 5 %RANDOM
Rwork0.15526 ---
obs0.15641 69108 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.126 Å2
Baniso -1Baniso -2Baniso -3
1-4.84 Å20 Å20 Å2
2--4.84 Å20 Å2
3----9.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8946 0 35 251 9232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219227
X-RAY DIFFRACTIONr_bond_other_d0.0090.0219227
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9412531
X-RAY DIFFRACTIONr_angle_other_deg1.2021.9412531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0551135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97923.634476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.527151401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6311566
X-RAY DIFFRACTIONr_chiral_restr0.0770.21293
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217311
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5571.55628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0428976
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4933599
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3474.53554
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 262 -
Rwork0.173 4821 -
obs--93.13 %
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)
10.79550.28180.12740.74570.04651.25590.0466-0.03510.0073-0.0270.0156-0.09590.02730.0701-0.06220.02390.01470.0220.0399-0.02320.0916-29.742631.257133.5676
20.3905-0.0392-0.07181.17510.24291.02950.0547-0.0391-0.02490.00330.0016-0.0930.03740.115-0.05620.0157-0.0006-0.02710.05350.0020.0857-21.788651.322672.2385
31.18290.312-0.03230.5835-0.11960.7167-0.0370.05640.02590.07060.1122-0.0798-0.06420.0198-0.07520.0309-0.00040.01480.0362-0.04880.0933-5.284928.61850.6894
40.9176-0.45250.08811.0195-0.00431.33210.00220.03790.08890.02180.06950.0105-0.00420.0009-0.07170.02840.00140.03540.0140.01660.082516.082524.3217-38.1915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 174
2X-RAY DIFFRACTION1A175 - 245
3X-RAY DIFFRACTION1A246 - 288
4X-RAY DIFFRACTION2B2 - 174
5X-RAY DIFFRACTION2B175 - 245
6X-RAY DIFFRACTION2B246 - 287
7X-RAY DIFFRACTION3C2 - 174
8X-RAY DIFFRACTION3C175 - 245
9X-RAY DIFFRACTION3C246 - 285
10X-RAY DIFFRACTION4D2 - 174
11X-RAY DIFFRACTION4D175 - 245
12X-RAY DIFFRACTION4D246 - 286

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