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- PDB-7n7z: Structure of Acetyl-CoA acetyltransferase from Syntrophomonas wolfei -

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Basic information

Entry
Database: PDB / ID: 7n7z
TitleStructure of Acetyl-CoA acetyltransferase from Syntrophomonas wolfei
ComponentsAcetyl-CoA C-acetyltransferase
KeywordsTRANSFERASE / Acetyl-CoA / Syntroph
Function / homologyacetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / Acetyl-CoA C-acetyltransferase
Function and homology information
Biological speciesSyntrophomonas wolfei subsp. wolfei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsArbing, M.A. / Gunsalus, R.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)447147-EL-21341 United States
CitationJournal: Front Microbiol / Year: 2022
Title: Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei.
Authors: Fu, J.Y. / Muroski, J.M. / Arbing, M.A. / Salguero, J.A. / Wofford, N.Q. / McInerney, M.J. / Gunsalus, R.P. / Loo, J.A. / Ogorzalek Loo, R.R.
History
DepositionJun 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,5362
Polymers84,5362
Non-polymers00
Water3,945219
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)169,0724
Polymers169,0724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area14550 Å2
ΔGint-40 kcal/mol
Surface area47410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.070, 81.070, 242.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Acetyl-CoA C-acetyltransferase /


Mass: 42268.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen) (bacteria)
Strain: DSM 2245B / Goettingen / Gene: Swol_0675 / Plasmid: pMAPLe4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0AZ52, acetyl-CoA C-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein buffer: 20 mM Tris pH 8, 150 mM NaCl, 5 mM B-ME. Crystallization buffer: 0.1 M Sodium formate pH 7.0, 12% PEG 3350. Cryo buffer: 23% PEG 3350, 5% PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.02→41.64 Å / Num. obs: 53598 / % possible obs: 99.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 33 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1041 / Rpim(I) all: 0.04584 / Rrim(I) all: 0.1141 / Net I/σ(I): 10.47
Reflection shellResolution: 2.02→2.094 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.8022 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 5118 / CC1/2: 0.511 / CC star: 0.822 / Rpim(I) all: 0.3867 / Rrim(I) all: 0.8933 / % possible all: 96.93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSVERSION OCT 15, 2015data reduction
XSCALEVERSION OCT 15, 2015data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WYS

4wys


Resolution: 2.02→41.64 Å / SU ML: 0.3131 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2742 5360 10 %
Rwork0.2327 48238 -
obs0.2369 53598 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.66 Å2
Refinement stepCycle: LAST / Resolution: 2.02→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 0 219 5987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195843
X-RAY DIFFRACTIONf_angle_d0.47997895
X-RAY DIFFRACTIONf_chiral_restr0.0417921
X-RAY DIFFRACTIONf_plane_restr0.00251028
X-RAY DIFFRACTIONf_dihedral_angle_d5.0883840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.050.38861620.35341462X-RAY DIFFRACTION91.24
2.05-2.070.42021720.33521550X-RAY DIFFRACTION99.77
2.07-2.090.39861780.32921594X-RAY DIFFRACTION99.94
2.09-2.120.36571760.31391590X-RAY DIFFRACTION99.94
2.12-2.150.36931750.31321577X-RAY DIFFRACTION99.72
2.15-2.180.33721770.30581587X-RAY DIFFRACTION99.72
2.18-2.210.34741780.30181600X-RAY DIFFRACTION99.94
2.21-2.240.33641760.30221583X-RAY DIFFRACTION100
2.24-2.280.33541730.28821562X-RAY DIFFRACTION99.77
2.28-2.310.32641800.28161618X-RAY DIFFRACTION99.89
2.31-2.350.3561750.26871577X-RAY DIFFRACTION100
2.35-2.40.32711790.27571613X-RAY DIFFRACTION100
2.4-2.440.3261770.27821588X-RAY DIFFRACTION100
2.44-2.490.36411770.27151594X-RAY DIFFRACTION100
2.49-2.550.29621780.25511603X-RAY DIFFRACTION99.39
2.55-2.610.31541770.26621596X-RAY DIFFRACTION99.55
2.61-2.670.31461770.26121588X-RAY DIFFRACTION99.77
2.67-2.740.29381780.25811606X-RAY DIFFRACTION100
2.74-2.820.29781780.24341605X-RAY DIFFRACTION99.94
2.83-2.920.31721810.24011623X-RAY DIFFRACTION100
2.92-3.020.28531800.24631617X-RAY DIFFRACTION99.94
3.02-3.140.29941780.25521605X-RAY DIFFRACTION99.89
3.14-3.280.29391810.25831627X-RAY DIFFRACTION99.94
3.28-3.460.29451790.22521614X-RAY DIFFRACTION99.83
3.46-3.670.2541820.22411641X-RAY DIFFRACTION99.89
3.67-3.960.24111820.20691640X-RAY DIFFRACTION99.84
3.96-4.350.20891850.18861658X-RAY DIFFRACTION99.78
4.36-4.980.1991810.17591631X-RAY DIFFRACTION97.58
4.99-6.280.25821870.19291680X-RAY DIFFRACTION98.63
6.28-41.640.21562010.19071809X-RAY DIFFRACTION99.11
Refinement TLS params.Method: refined / Origin x: 50.7728525071 Å / Origin y: 79.4941478838 Å / Origin z: 102.708502199 Å
111213212223313233
T0.272282728895 Å2-0.012880104467 Å2-0.051167941378 Å2-0.240978290713 Å20.0798945712271 Å2--0.277441096687 Å2
L0.493947750754 °20.189150731597 °2-0.0924547927921 °2-1.32201085248 °2-0.237576126359 °2--0.72423314868 °2
S-0.0272436560345 Å °0.0807465503042 Å °0.040706340529 Å °-0.183617493862 Å °0.055675443534 Å °0.0841824024723 Å °0.0246529347876 Å °-0.0904038536593 Å °-0.0284855734642 Å °
Refinement TLS groupSelection details: all

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