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- PDB-8jg3: Biosynthetic thiolase from Clostridium kluyveri -

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Basic information

Entry
Database: PDB / ID: 8jg3
TitleBiosynthetic thiolase from Clostridium kluyveri
ComponentsAcetyl-CoA C-acetyltransferase
KeywordsBIOSYNTHETIC PROTEIN / biosynthetic thiolase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups
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-like
Similarity search - Domain/homology
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesClostridium kluyveri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, E.-J. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of biosynthetic thiolase from Clostridium kluyveri
Authors: Jeon, B.S. / Kim, E.-J. / Kim, K.-J. / Sang, B.-I.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA C-acetyltransferase
B: Acetyl-CoA C-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)85,2322
Polymers85,2322
Non-polymers00
Water1,910106
1
A: Acetyl-CoA C-acetyltransferase
B: Acetyl-CoA C-acetyltransferase

A: Acetyl-CoA C-acetyltransferase
B: Acetyl-CoA C-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)170,4634
Polymers170,4634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area14380 Å2
ΔGint-63 kcal/mol
Surface area47860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.568, 73.568, 273.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetyl-CoA C-acetyltransferase


Mass: 42615.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium kluyveri (bacteria) / Gene: CKR_3261 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B9DX69
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Description: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 and 0.2M Ammonium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2015
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→46.7 Å / Num. obs: 58118 / % possible obs: 97.78 % / Redundancy: 2 % / Biso Wilson estimate: 28.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03003 / Rpim(I) all: 0.03003 / Rrim(I) all: 0.04246 / Net I/σ(I): 20.85
Reflection shellResolution: 2→2.071 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3493 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4835 / CC1/2: 0.663 / CC star: 0.893 / Rpim(I) all: 0.3493 / Rrim(I) all: 0.494 / % possible all: 82.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.65 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.003 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23954 2011 3.5 %RANDOM
Rwork0.20853 ---
obs0.20962 56112 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.901 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5686 0 0 106 5792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165706
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6327796
X-RAY DIFFRACTIONr_angle_other_deg0.4751.5713137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.399527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.939101000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
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_it2.423.1073080
X-RAY DIFFRACTIONr_mcbond_other2.423.1073080
X-RAY DIFFRACTIONr_mcangle_it3.2855.5733843
X-RAY DIFFRACTIONr_mcangle_other3.2855.5733844
X-RAY DIFFRACTIONr_scbond_it3.3183.5172691
X-RAY DIFFRACTIONr_scbond_other3.3173.5182692
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0076.2953954
X-RAY DIFFRACTIONr_long_range_B_refined5.56128.726256
X-RAY DIFFRACTIONr_long_range_B_other5.56128.696244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 125 -
Rwork0.314 3336 -
obs--79.99 %

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