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- PDB-5lp7: Crystal structure of 3-Ketoacyl-CoA Thiolase (MmgA) from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5lp7
TitleCrystal structure of 3-Ketoacyl-CoA Thiolase (MmgA) from Bacillus subtilis.
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / Thiolase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / sporulation resulting in formation of a cellular spore / cytoplasm
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBaker, G.E. / Race, P.R.
CitationJournal: To Be Published
Title: Crystal structure of 3-Ketoacyl-CoA Thiolase (MmgA) from Bacillus subtilis.
Authors: Baker, G.E. / Race, P.R.
History
DepositionAug 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
H: Acetyl-CoA acetyltransferase
E: Acetyl-CoA acetyltransferase
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
F: Acetyl-CoA acetyltransferase
G: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,54616
Polymers329,8098
Non-polymers7378
Water15,817878
1
H: Acetyl-CoA acetyltransferase
E: Acetyl-CoA acetyltransferase
F: Acetyl-CoA acetyltransferase
G: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1817
Polymers164,9054
Non-polymers2763
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-63 kcal/mol
Surface area49250 Å2
MethodPISA
2
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,3659
Polymers164,9054
Non-polymers4605
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15310 Å2
ΔGint-64 kcal/mol
Surface area48570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.180, 141.120, 211.462
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase / 3-Ketoacyl-CoA Thiolase


Mass: 41226.168 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: mmgA, yqiL, BSU24170 / Production host: Escherichia coli (E. coli) / References: UniProt: P45855, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium iodide, 0.1 M BTP pH 8.5, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.425
11-h,-k,l20.575
ReflectionResolution: 2.2→33.91 Å / Num. all: 497070 / Num. obs: 161184 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.2→31.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.857 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20461 8412 4.9 %RANDOM
Rwork0.15011 ---
obs0.15282 153197 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å21.32 Å2
2--1.48 Å20 Å2
3----4.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21815 0 48 878 22741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01923011
X-RAY DIFFRACTIONr_bond_other_d0.0030.0222310
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.97231022
X-RAY DIFFRACTIONr_angle_other_deg1.224351154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.26453088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70424.585855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.586153615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.09315141
X-RAY DIFFRACTIONr_chiral_restr0.1690.23575
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0226369
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024836
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_it1.772.05612437
X-RAY DIFFRACTIONr_mcbond_other1.7692.05612436
X-RAY DIFFRACTIONr_mcangle_it2.663.07615494
X-RAY DIFFRACTIONr_mcangle_other2.663.07615495
X-RAY DIFFRACTIONr_scbond_it2.0142.26410574
X-RAY DIFFRACTIONr_scbond_other2.0142.26410575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9863.31415529
X-RAY DIFFRACTIONr_long_range_B_refined5.01516.71326154
X-RAY DIFFRACTIONr_long_range_B_other5.01516.71326155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.159→2.215 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 592 -
Rwork0.237 11833 -
obs--96.65 %

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