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- PDB-3bal: Crystal Structure of an Acetylacetone Dioxygenase from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 3bal
TitleCrystal Structure of an Acetylacetone Dioxygenase from Acinetobacter johnsonii
ComponentsAcetylacetone-cleaving enzyme
KeywordsOXIDOREDUCTASE / JELLY ROLL / TETRAMER / Dioxygenase / Iron / Metal-binding
Function / homology
Function and homology information


acetylacetone-cleaving enzyme / acetylacetone-cleaving enzyme activity / metal ion binding
Similarity search - Function
ChrR-like cupin domain / ChrR Cupin-like domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Acetylacetone-cleaving enzyme
Similarity search - Component
Biological speciesAcinetobacter johnsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsStranzl, G.R. / Wagner, U.G. / Straganz, G. / Steiner, W. / Kratky, C.
CitationJournal: To be Published
Title: Crystal Structure of an Acetylacetone Dioxygenase from Acinetobacter johnsonii
Authors: Stranzl, G.R. / Wagner, U.G. / Straganz, G. / Steiner, W. / Kratky, C.
History
DepositionNov 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Acetylacetone-cleaving enzyme
B: Acetylacetone-cleaving enzyme
C: Acetylacetone-cleaving enzyme
D: Acetylacetone-cleaving enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7478
Polymers66,4854
Non-polymers2624
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-208 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.200, 57.200, 62.930
Angle α, β, γ (deg.)69.850, 74.320, 69.710
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Acetylacetone-cleaving enzyme / Acetylacetone dioxygenase / Diketone cleaving dioxygenase / Diketone cleaving enzyme


Mass: 16621.279 Da / Num. of mol.: 4 / Fragment: ACETYLACETONE DIOXYGENASE / Source method: isolated from a natural source / Source: (natural) Acinetobacter johnsonii (bacteria) / References: UniProt: Q8GNT2, acetylacetone-cleaving enzyme
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris HCl, 40% PEG 3350, 0.2M Sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1310.8033
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.0000, 1.2847, 1.2840
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJun 24, 2001
MAR CCD 165 mm2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.80331
211
31.28471
41.2841
ReflectionAv σ(I) over netI: 13.1 / Number: 104251 / Rmerge(I) obs: 0.053 / Χ2: 1.15 / D res high: 1.95 Å / D res low: 25 Å / Num. obs: 36543 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.82598.710.0381.506
3.814.898.610.0371.26
3.333.8198.210.0431.235
3.033.3397.810.0471.205
2.813.0397.210.0521.255
2.652.8197.110.0571.207
2.512.6596.510.0621.085
2.42.5196.210.0741.174
2.312.49610.0771.119
2.232.3195.610.0881.139
2.162.2395.810.0941.066
2.12.1694.910.0971.005
2.052.194.710.1151.051
22.0594.510.1230.991
1.9529410.1440.901
ReflectionResolution: 1.95→25 Å / Num. obs: 37241 / % possible obs: 97.8 % / Rmerge(I) obs: 0.036 / Χ2: 0.96 / Net I/σ(I): 16.1
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.113 / Num. unique all: 2245 / Χ2: 0.613 / % possible all: 88.2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 1.9 Å / D res low: 25 Å / FOM : 0.39 / Reflection: 36273
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.2844.82-6.76
13 wavelength21.28470.47-7.26
13 wavelength312.64-1.53
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1LAM1150.999011.039
2LAM1150.9590.3920.4241.085
3LAM1150.0080.4970.9821.125
4LAM1150.520.9150.3461.016
Phasing MAD shell
Resolution (Å)FOM Reflection
6.77-250.61823
4.3-6.770.493200
3.37-4.30.454074
2.86-3.370.484764
2.53-2.860.435319
2.29-2.530.375890
2.11-2.290.286215
1.96-2.110.224988
Phasing dmFOM : 0 / FOM acentric: 0 / FOM centric: 0 / Reflection acentric: 0 / Reflection centric: 0
Phasing dm shell
Resolution (Å)
5.5-24.576
3.4-5.5
2.7-3.4
2.4-2.7
2.1-2.4
1.9-2.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE1.18phasing
RESOLVE1.05phasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→25 Å / FOM work R set: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3684 0 %RANDOM
Rwork0.183 ---
obs-36795 96.6 %-
Solvent computationBsol: 49.042 Å2
Displacement parametersBiso mean: 20.486 Å2
Baniso -1Baniso -2Baniso -3
1--5.661 Å2-0.318 Å20.995 Å2
2--3.321 Å2-1.201 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 4 461 5053
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.336
X-RAY DIFFRACTIONc_mcbond_it1.1211.5
X-RAY DIFFRACTIONc_scbond_it1.8452
X-RAY DIFFRACTIONc_mcangle_it1.7722
X-RAY DIFFRACTIONc_scangle_it2.6942.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5but.parambut.top

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