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- PDB-3bh2: Structural Studies of Acetoacetate Decarboxylase -

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Basic information

Entry
Database: PDB / ID: 3bh2
TitleStructural Studies of Acetoacetate Decarboxylase
ComponentsAcetoacetate decarboxylase
KeywordsLYASE / acetoacetate decarboxylase / Plasmid / Schiff base
Function / homology
Function and homology information


acetoacetate decarboxylase / acetoacetate decarboxylase activity / identical protein binding
Similarity search - Function
Acetoacetate decarboxylase, bacterial / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase / Acetoacetate decarboxylase domain superfamily / Acetoacetate decarboxylase (ADC) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Acetoacetate decarboxylase
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHo, M. / Allen, K.N.
CitationJournal: Nature / Year: 2009
Title: The origin of the electrostatic perturbation in acetoacetate decarboxylase.
Authors: Ho, M.C. / Menetret, J.F. / Tsuruta, H. / Allen, K.N.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999 SEQUENCE AUTHORS STATE THAT THE MUTATION L2V HAS BEEN INTRODUCED FOR CLONING PURPOSE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)110,2274
Polymers110,2274
Non-polymers00
Water5,747319
1
A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase

A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase

A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)330,68212
Polymers330,68212
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area52690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.070, 104.070, 578.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Acetoacetate decarboxylase / ADC / AAD


Mass: 27556.803 Da / Num. of mol.: 4 / Mutation: L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: adc, CA_P0165 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23670, acetoacetate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.95
Details: 40mM Phosphate buffer pH 5.95, 100mM Sarcosine, 15% PEG 3350, 18% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 47172 / % possible obs: 98.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.51 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.4 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.652 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24429 4638 10.1 %RANDOM
Rwork0.19581 ---
obs0.20064 41399 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7770 0 0 319 8089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.98510823
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0324340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.641151374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9081544
X-RAY DIFFRACTIONr_chiral_restr0.0810.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23538
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25273
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.2164
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.411.55086
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71128027
X-RAY DIFFRACTIONr_scbond_it1.1433266
X-RAY DIFFRACTIONr_scangle_it1.9264.52796
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 282 -
Rwork0.253 2594 -
obs--93.1 %

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