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- PDB-3bh3: Crystal structure of acetoacetate decarboxylase from Chromobacter... -

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Basic information

Entry
Database: PDB / ID: 3bh3
TitleCrystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediate
ComponentsAcetoacetate decarboxylase
KeywordsLYASE / acetoacetate decarboxylase / Schiff base intermediate
Function / homology
Function and homology information


acetoacetate decarboxylase / acetoacetate decarboxylase activity
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
pentan-2-one / Acetoacetate decarboxylase
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6628
Polymers109,3184
Non-polymers3454
Water7,206400
1
A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase
hetero molecules

A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase
hetero molecules

A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,98724
Polymers327,95312
Non-polymers1,03412
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 area48390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.661, 105.661, 252.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Acetoacetate decarboxylase / ADC / AAD


Mass: 27329.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: DSM 30191 / IFO 12614 / JCM 1249 / NCIB 9131 / Gene: adc, CV_3520 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NSA6, acetoacetate decarboxylase
#2: Chemical
ChemComp-PNH / pentan-2-one


Mass: 86.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.5M Potassium phoshpate dibasic/Sodium phosphate monobasic, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 60919 / % possible obs: 99.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.4
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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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: 2.1→28.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25094 3091 5.1 %RANDOM
Rwork0.19583 ---
obs0.19868 57827 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.137 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7690 0 24 400 8114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9910801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0285977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.01822.448339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.199151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5371568
X-RAY DIFFRACTIONr_chiral_restr0.1030.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.23561
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25209
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6791.54929
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20427982
X-RAY DIFFRACTIONr_scbond_it1.84732999
X-RAY DIFFRACTIONr_scangle_it2.9464.52819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 208 -
Rwork0.286 4330 -
obs--100 %

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