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- PDB-4egv: Crystal structure of a monomeric SCP2-thiolase like protein type ... -

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Basic information

Entry
Database: PDB / ID: 4egv
TitleCrystal structure of a monomeric SCP2-thiolase like protein type 1 (STLP1) from Mycobacterium smegmatis
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / new sub-family / Thiolase fold
Function / homology
Function and homology information


transferase activity
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #840 / Thiolase-like protein type 1, additional C-terminal domain / Thiolase-like protein type 1 additional C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsJanardan, N. / Harijan, R.K. / Wierenga, R.K. / Murthy, M.R.N.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of a Monomeric Thiolase-Like Protein Type 1 (TLP1) from Mycobacterium smegmatis.
Authors: Janardan, N. / Harijan, R.K. / Wierenga, R.K. / Murthy, M.R.N.
History
DepositionApr 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references / Derived calculations
Category: reflns_shell / struct_conn / struct_ref_seq_dif
Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low ..._reflns_shell.d_res_high / _reflns_shell.d_res_low / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
E: Acetyl-CoA acetyltransferase
F: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)337,1946
Polymers337,1946
Non-polymers00
Water2,882160
1
A: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1991
Polymers56,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1991
Polymers56,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1991
Polymers56,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1991
Polymers56,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1991
Polymers56,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1991
Polymers56,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.308, 102.004, 102.423
Angle α, β, γ (deg.)116.46, 101.28, 97.44
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 507
2111B1 - 507
3111C1 - 507
4111D1 - 507
5111E1 - 507
6111F2 - 507

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Components

#1: Protein
Acetyl-CoA acetyltransferase


Mass: 56198.949 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_5521 / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / References: UniProt: A0R3M0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.54 Å3/Da / Density % sol: 51.55 % / Description: THE FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: 100mM HEPES pH 7.5, 20% PEG 4000, 10% isopropanol, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9789 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 26, 2010
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 83286 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID
2.6-2.642.80.32.31
2.64-2.73.70.42.51
2.7-2.752.80.44.61

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXDphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.71→47.95 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.891 / SU B: 14.268 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 3.111 / ESU R Free: 0.361
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: THE FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26107 4398 5 %RANDOM
Rwork0.23354 ---
obs0.23492 83286 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.718 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.02 Å20.03 Å2
2--0.02 Å20.03 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.71→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20012 0 0 160 20172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02220783
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.96628238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55952733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29624.122871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.239153245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.79315145
X-RAY DIFFRACTIONr_chiral_restr0.1460.23244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115854
X-RAY DIFFRACTIONr_mcbond_it0.7671.513637
X-RAY DIFFRACTIONr_mcangle_it1.48221732
X-RAY DIFFRACTIONr_scbond_it1.98637146
X-RAY DIFFRACTIONr_scangle_it3.4584.56498
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3221 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.090.05
Btight positional0.070.05
Ctight positional0.070.05
Dtight positional0.080.05
Etight positional0.090.05
Ftight positional0.080.05
Atight thermal0.130.5
Btight thermal0.120.5
Ctight thermal0.130.5
Dtight thermal0.130.5
Etight thermal0.120.5
Ftight thermal0.130.5
LS refinement shellResolution: 2.706→2.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 279 -
Rwork0.396 5355 -
obs--84.65 %

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