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- PDB-1f1x: CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM BRE... -

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Basic information

Entry
Database: PDB / ID: 1f1x
TitleCRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM BREVIBACTERIUM FUSCUM
ComponentsHOMOPROTOCATECHUATE 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / Dioxygenase / Extradiol / Iron / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
HYDRATED FE / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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: J.Biol.Chem. / Year: 1996
Title: Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum. A Dioxygenase with Catalase Activity.
Authors: Miller, M.A. / Lipscomb, J.D.
#2: Journal: Protein Expr.Purif. / Year: 1997
Title: Cloning, overexpression, and mutagenesis of the gene for homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum.
Authors: Wang, Y.Z. / Lipscomb, J.D.
History
DepositionMay 20, 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: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
C: HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
D: HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0868
Polymers148,6464
Non-polymers4404
Water19,6901093
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-72 kcal/mol
Surface area41930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.100, 157.100, 121.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsThe biological assembly is a tetramer. There is a tetramer per asymmetric unit.

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Components

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


Mass: 37161.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase
#2: Chemical
ChemComp-FEL / HYDRATED FE


Mass: 109.891 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: FeH6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1093 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 298 K / Method: batch crystallization / pH: 7.5
Details: Peg5000, Mg Acetate, MOPS, Glycerol was add prior to data collection., pH 7.5, Batch crystallization, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mg/mlprotein1drop
210-15 %PEG5000 MME1reservoir
30.2 Mmagnesium acetate1reservoir
4100 mMMOPS1reservoirpH7.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.032
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 7, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.032 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 234020 / Num. obs: 216266 / % possible obs: 92.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.54 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 20
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.094 / Num. unique all: 19027 / % possible all: 81.2
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 92.9 % / Redundancy: 2.55 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 79.5 % / Redundancy: 1.51 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementResolution: 1.6→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 18094 -Random 10%
Rwork0.168 ---
all0.168 193205 --
obs0.168 181799 94.1 %-
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10432 0 16 1093 11541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.13669
X-RAY DIFFRACTIONc_bond_d0.022812
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_d0.023
X-RAY DIFFRACTIONc_angle_deg2.14
LS refinement shell
*PLUS
Rfactor Rfree: 0.239 / Rfactor Rwork: 0.187

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