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- PDB-1f1r: CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ART... -

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Basic information

Entry
Database: PDB / ID: 1f1r
TitleCRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS (NATIVE, NON-CRYO)
ComponentsHOMOPROTOCATECHUATE 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / Dioxygenase / Extradiol / Manganese / Biodegradation / Aromatic
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / : / 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 ...3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / : / 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
: / 3,4-dihydroxyphenylacetate 2,3-dioxygenase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsVetting, M.W. / Lipscomb, J.D. / Wackett, L.P. / Que Jr., L. / Ohlendorf, D.H.
Citation
Journal: J.Bacteriol. / Year: 2004
Title: Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.
Authors: Vetting, M.W. / Wackett, L.P. / Que Jr., L. / Lipscomb, J.D. / Ohlendorf, D.H.
#1: Journal: Biochemistry / Year: 1996
Title: Manganese(II)-dependent Extradiol-cleaving Catechol Dioxygenase from Arthrobacter globiformis CM-2
Authors: Whiting, A.K. / Boldt, Y.R. / Hendrich, M.P. / Wackett, L.P. / Que Jr, L.
#2: Journal: J.BACTERIOL. / Year: 1995
Title: A Manganese-dependent Dioxygenase from Arthrobacter globiformis CM-2 belongs to the Major Extradiol Dioxygenase Family
Authors: Boldt, Y.R. / Sadowsky, M.J. / Ellis, L.B. / Que Jr, L. / Wackett, L.P.
#3: Journal: Biochemistry / Year: 1997
Title: Manganese(II) Active Site Mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis Strain CM-2.
Authors: Boldt, Y.R. / Whiting, A.K. / Wagner, M.L. / Sadowsky, M.J. / Que Jr, L. / Wackett, L.P.
#4: Journal: J.Biol.Chem. / Year: 1981
Title: 3,4-Dihydroxyphenylacetate 2,3-dioxygenase. A Manganese(II) Dioxygenase from Bacillus brevis.
Authors: Que Jr, L. / Widom, J. / Crawford, R.L.
History
DepositionMay 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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 / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
B: HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0944
Polymers73,9842
Non-polymers1102
Water6,323351
1
A: HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
B: HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)148,1898
Polymers147,9694
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11670 Å2
ΔGint-71 kcal/mol
Surface area41890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.440, 59.150, 102.800
Angle α, β, γ (deg.)90.00, 118.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

DetailsThe biological assembly is a tetramer constructed from chain A and chain B with a symmetry partner generated by the two-fold.

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Components

#1: Protein HOMOPROTOCATECHUATE 2,3-DIOXYGENASE / 3 / 4-DIHYDROXYPHENYLACETATE 2 / 3-DIOXYGENASE


Mass: 36992.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Strain: CM-2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q44048, 3,4-dihydroxyphenylacetate 2,3-dioxygenase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 298 K / pH: 6.8
Details: Peg 8000, Mg Acetate, Na cacodylate, pH 6.8, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mg/mlprotein11
26-10 %PEG800012
30.2 Mmagnesium acetate12
4100 mMsodium cacodylate12pH6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 60397 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.53 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.42 % / Rmerge(I) obs: 0.01 / Num. unique all: 10808 / % possible all: 87.1
Reflection
*PLUS
Highest resolution: 1.75 Å / % possible obs: 88.7 % / Redundancy: 2.6 %
Reflection shell
*PLUS
% possible obs: 65 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 1

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Processing

Software
NameClassification
X-GENdata reduction
CNSrefinement
X-GENdata scaling
CNSphasing
RefinementResolution: 1.8→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.187 6105 -Random 10%
Rwork0.156 ---
all0.156 68087 --
obs0.156 60397 88.7 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 2 351 5547
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.020093
X-RAY DIFFRACTIONc_angle_deg2.02342
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
LS refinement shell
*PLUS
Rfactor Rfree: 0.298 / Rfactor Rwork: 0.265

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