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- PDB-4p9g: Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alca... -

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Basic information

Entry
Database: PDB / ID: 4p9g
TitleStructure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp.
Components2,4'-dihydroxyacetophenone dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / cupin-fold / iron-binding / carbonate
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
CARBONATE ION / : / 2,4'-dihydroxyacetophenone dioxygenase
Similarity search - Component
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKeegan, R. / Lebedev, A. / Erskine, P. / Guo, J. / Wood, S.P. / Hopper, D.J. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP
Authors: Keegan, R. / Lebedev, A. / Erskine, P. / Guo, J. / Wood, S.P. / Hopper, D.J. / Rigby, S.E.J. / Cooper, J.B.
History
DepositionApr 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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)22,8984
Polymers22,6901
Non-polymers2083
Water2,126118
1
A: 2,4'-dihydroxyacetophenone dioxygenase
hetero molecules

A: 2,4'-dihydroxyacetophenone dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7978
Polymers45,3812
Non-polymers4166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3660 Å2
ΔGint-52 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.557, 82.557, 114.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 2,4'-dihydroxyacetophenone dioxygenase


Mass: 22690.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal portion could not be defined in the electron density map.
Source: (gene. exp.) Alcaligenes sp. (bacteria) / Gene: dad / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.48 Å3/Da / Density % sol: 56 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop ...Details: Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop crystallisation trials. Well solution: 10 % w/v PEG 1k and 10 % PEG 10k (Molecular Dimensions Structure Screen 2, condition 46).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.072 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.2→57 Å / Num. obs: 10549 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.1 / % possible all: 49.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
BALBESphasing
MOLREPphasing
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ebr, 2oq1, 3bal, 3cjx

3ebr

2oq1

3bal

3cjx


Resolution: 2.2→71.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.732 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21758 512 4.9 %RANDOM
Rwork0.17342 ---
obs0.17564 10021 86.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.697 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.05 Å2
Refine analyzeLuzzati sigma a obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 2.2→71.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 11 118 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.921783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.775153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01822.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.20115189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9561510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211050
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 18 -
Rwork0.243 339 -
obs--43.17 %
Refinement TLS params.Method: refined / Origin x: 24.2114 Å / Origin y: 20.6134 Å / Origin z: 5.8224 Å
111213212223313233
T0.0217 Å20.0036 Å2-0.0023 Å2-0.0205 Å20.015 Å2--0.0141 Å2
L0.4367 °20.1227 °2-0.1783 °2-0.2933 °2-0.046 °2--0.7827 °2
S0.0256 Å °0.0104 Å °0.0146 Å °-0.005 Å °0.0345 Å °0.0216 Å °-0.0069 Å °-0.0437 Å °-0.0601 Å °

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