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- PDB-7yvy: Crystal structure of thiolase PFC_04095 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 7yvy
TitleCrystal structure of thiolase PFC_04095 from Pyrococcus furiosus
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / Pyrococcus furiosus / acetoacetyl-CoA thiolase / acetyl-CoA acetyltransferase
Function / homologyThiolase C-terminal domain-like / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / Acetyl-CoA acetyltransferase
Function and homology information
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, R. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR40990/MED/29/1540/2020 India
CitationJournal: To Be Published
Title: Crystal structure of thiolase PFC_04095 from Pyrococcus furiosus
Authors: Singh, R. / Das, A.K.
History
DepositionAug 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,0603
Polymers123,0603
Non-polymers00
Water00
1
A: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,0201
Polymers41,0201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,0201
Polymers41,0201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,0201
Polymers41,0201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.246, 113.482, 107.533
Angle α, β, γ (deg.)90.000, 123.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 41019.887 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_04095 / Production host: Escherichia coli (E. coli) / References: UniProt: I6V154, acetyl-CoA C-acetyltransferase

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M carboxylic acids, 0.1 M buffer system 3 pH 8.5 and 50 % v/v precipitant mix 4. Carboxylic acids: 0.2 M each of sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, ...Details: 0.1 M carboxylic acids, 0.1 M buffer system 3 pH 8.5 and 50 % v/v precipitant mix 4. Carboxylic acids: 0.2 M each of sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate. Buffer system 3: Tris (base); bicine pH 8.5 Precipitant mix 4: MPD_PIK_P3350 (25 % v/v MPD, 25 % PEG 1000, 25 % w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.7→48.03 Å / Num. obs: 36797 / % possible obs: 99.24 % / Redundancy: 6.7 % / Biso Wilson estimate: 77.7 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 16.93
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 3666 / CC1/2: 0.923 / CC star: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ESQ

6esq


Resolution: 2.7→48.03 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1814 4.95 %
Rwork0.2092 34840 -
obs0.2114 36654 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.95 Å2 / Biso mean: 91.3016 Å2 / Biso min: 43.15 Å2
Refinement stepCycle: final / Resolution: 2.7→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7760 0 0 0 7760
Num. residues----1091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.770.37911430.34412630277398
2.77-2.850.35931440.29652651279599
2.85-2.950.35221350.28492661279699
2.95-3.050.33541310.28552678280999
3.05-3.170.41331240.32512683280799
3.17-3.320.361200.28752676279699
3.32-3.490.29121680.25832654282299
3.49-3.710.2841330.24422680281399
3.71-40.28881320.21192692282499
4-4.40.22231320.172727022834100
4.4-5.040.20891600.171326762836100
5.04-6.340.23231450.197527172862100
6.35-48.030.19551470.169427402887100
Refinement TLS params.Method: refined / Origin x: 25.671 Å / Origin y: -33.553 Å / Origin z: -7.7945 Å
111213212223313233
T0.5184 Å2-0.013 Å2-0.0017 Å2-0.4588 Å2-0.0249 Å2--0.4969 Å2
L0.6306 °20.2825 °20.0317 °2-0.1392 °20.0306 °2---0.1058 °2
S-0.0332 Å °0.0807 Å °0.1096 Å °-0.0563 Å °0.0391 Å °-0.1379 Å °-0.0687 Å °-0.011 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 388
2X-RAY DIFFRACTION1allB1 - 388
3X-RAY DIFFRACTION1allC2 - 387

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