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- PDB-5bpx: Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alca... -

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Basic information

Entry
Database: PDB / ID: 5bpx
TitleStructure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP.
Components2,4'-dihydroxyacetophenone dioxygenase
KeywordsOXIDOREDUCTASE / rmlc-like cupin protein
Function / homology
Function and homology information


2,4'-dihydroxyacetophenone dioxygenase / 2,4'-dihydroxyacetophenone dioxygenase activity / metal ion binding
Similarity search - Function
ChrR-like cupin domain / ChrR Cupin-like domain / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / 2,4'-dihydroxyacetophenone dioxygenase
Similarity search - Component
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGuo, J. / Erskine, P. / Wood, S.P. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Extension of resolution and oligomerization-state studies of 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP.
Authors: Guo, J. / Erskine, P. / Coker, A.R. / Gor, J. / Perkins, S.J. / Wood, S.P. / Cooper, J.B.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Structure summary
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: 2,4'-dihydroxyacetophenone dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9514
Polymers17,7441
Non-polymers2073
Water2,576143
1
A: 2,4'-dihydroxyacetophenone dioxygenase
hetero molecules

A: 2,4'-dihydroxyacetophenone dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9028
Polymers35,4882
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area4100 Å2
ΔGint-57 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.250, 83.250, 114.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

#1: Protein 2,4'-dihydroxyacetophenone dioxygenase


Mass: 17743.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A catalytic ferrous ion is tightly bound in the active site.
Source: (gene. exp.) Alcaligenes sp. (bacteria) / Gene: dad / Production host: Escherichia coli (E. coli)
References: UniProt: Q9REI7, 2,4'-dihydroxyacetophenone dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.34 % / Description: long needles
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M sodium cacodylate pH 5.9 - 6.8. 1.1 - 1.6 M sodium acetate
PH range: 5.9 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.88→41.62 Å / Num. obs: 19556 / % possible obs: 99.5 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 21.8
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 5 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p9g

4p9g


Resolution: 1.88→41.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.911 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 938 4.8 %RANDOM
Rwork0.14195 ---
obs0.14345 18593 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.88→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1257 0 11 143 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191316
X-RAY DIFFRACTIONr_bond_other_d0.0020.021170
X-RAY DIFFRACTIONr_angle_refined_deg2.2331.921788
X-RAY DIFFRACTIONr_angle_other_deg1.80332684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.982370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47615189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.292159
X-RAY DIFFRACTIONr_chiral_restr0.1750.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
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_it2.542.026613
X-RAY DIFFRACTIONr_mcbond_other2.5312.024611
X-RAY DIFFRACTIONr_mcangle_it3.7033.018763
X-RAY DIFFRACTIONr_mcangle_other3.7023.019764
X-RAY DIFFRACTIONr_scbond_it5.4322.685703
X-RAY DIFFRACTIONr_scbond_other5.4282.685704
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3153.7871026
X-RAY DIFFRACTIONr_long_range_B_refined10.3218.8981531
X-RAY DIFFRACTIONr_long_range_B_other10.19118.2151475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 59 -
Rwork0.195 1324 -
obs--98.5 %

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