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- PDB-8rpk: AMP-forming Acetyl-CoA synthetase from Chloroflexota bacterium wi... -

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Basic information

Entry
Database: PDB / ID: 8rpk
TitleAMP-forming Acetyl-CoA synthetase from Chloroflexota bacterium without bound ligand
ComponentsAcetate--CoA ligase
KeywordsLIGASE / AcsA / CoA / phospho histidine
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding
Similarity search - Function
AMP-binding / Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase ...AMP-binding / Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
: / Acetate--CoA ligase
Similarity search - Component
Biological speciesChloroflexota bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.615 Å
AuthorsStriska, K. / Palm, G.J. / Lammers, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule.
Authors: Qin, C. / Graf, L.G. / Striska, K. / Janetzky, M. / Geist, N. / Specht, R. / Schulze, S. / Palm, G.J. / Girbardt, B. / Dorre, B. / Berndt, L. / Kemnitz, S. / Doerr, M. / Bornscheuer, U.T. / ...Authors: Qin, C. / Graf, L.G. / Striska, K. / Janetzky, M. / Geist, N. / Specht, R. / Schulze, S. / Palm, G.J. / Girbardt, B. / Dorre, B. / Berndt, L. / Kemnitz, S. / Doerr, M. / Bornscheuer, U.T. / Delcea, M. / Lammers, M.
History
DepositionJan 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetate--CoA ligase
B: Acetate--CoA ligase
C: Acetate--CoA ligase
D: Acetate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,6029
Polymers296,4664
Non-polymers1365
Water81145
1
A: Acetate--CoA ligase
hetero molecules

A: Acetate--CoA ligase
hetero molecules

A: Acetate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,5409
Polymers222,3503
Non-polymers1906
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
2
B: Acetate--CoA ligase
C: Acetate--CoA ligase
D: Acetate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4226
Polymers222,3503
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.352, 161.352, 814.182
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Acetate--CoA ligase


Mass: 74116.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexota bacterium (bacteria) / Gene: acs, E6J36_13485 / Details (production host): pET45(+) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A535FEC2, acetate-CoA ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 6, 2023 / Details: mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.615→272 Å / Num. obs: 100973 / % possible obs: 81.5 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.027 / Rrim(I) all: 0.122 / Net I/σ(I): 19.1
Reflection shellResolution: 2.62→2.82 Å / Redundancy: 20 % / Rmerge(I) obs: 1.952 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5050 / CC1/2: 0.711 / Rpim(I) all: 0.445 / Rrim(I) all: 2.002 / % possible all: 20.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDS20230630data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.615→272 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.92 / SU B: 24.464 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.533 / ESU R Free: 0.289
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2213 5010 4.962 %
Rwork0.1629 95963 -
all0.166 --
obs-100973 81.507 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 78.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.376 Å2-0.188 Å20 Å2
2---0.376 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.615→272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19896 0 5 45 19946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01220716
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619388
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.8328216
X-RAY DIFFRACTIONr_angle_other_deg0.6151.75744792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68952548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.8325140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.936103400
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.53510912
X-RAY DIFFRACTIONr_chiral_restr0.0820.23032
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024714
X-RAY DIFFRACTIONr_nbd_refined0.2160.23946
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.217964
X-RAY DIFFRACTIONr_nbtor_refined0.1880.29993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.210533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2388
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.221
X-RAY DIFFRACTIONr_nbd_other0.1780.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0960.25
X-RAY DIFFRACTIONr_mcbond_it4.6135.68910120
X-RAY DIFFRACTIONr_mcbond_other4.6135.68910120
X-RAY DIFFRACTIONr_mcangle_it6.45910.23412662
X-RAY DIFFRACTIONr_mcangle_other6.45910.23512663
X-RAY DIFFRACTIONr_scbond_it5.5036.05610596
X-RAY DIFFRACTIONr_scbond_other5.5026.05610597
X-RAY DIFFRACTIONr_scangle_it7.90310.95715544
X-RAY DIFFRACTIONr_scangle_other7.90310.95815545
X-RAY DIFFRACTIONr_lrange_it9.12752.98422438
X-RAY DIFFRACTIONr_lrange_other9.12752.98622438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.615-2.6830.374240.2875330.29191070.9370.9516.11620.286
2.683-2.7560.381700.30617420.30988030.9280.94920.58390.299
2.756-2.8360.3261680.30634900.30785960.9360.95242.55470.298
2.836-2.9230.3433730.28568130.28883640.9330.95785.91580.274
2.923-3.0190.2933910.25877010.25981070.9440.96299.8150.241
3.019-3.1250.3223730.23674680.2478410.9360.9671000.215
3.125-3.2430.2713800.2171950.21375760.950.97499.98680.19
3.243-3.3760.2543680.19469390.19773070.9570.9771000.177
3.376-3.5260.2743370.19566740.19970110.9560.9791000.18
3.526-3.6980.2672940.18555390.18967170.9550.9886.83940.169
3.698-3.8980.2372930.16359390.16763890.9660.98597.54260.153
3.898-4.1340.193110.1455700.14360740.9770.98996.82250.133
4.134-4.420.1662760.12554080.12756850.9830.99199.98240.122
4.42-4.7740.1732870.11250540.11553420.9830.99299.98130.111
4.774-5.2290.162370.11246810.11449180.9850.9931000.113
5.229-5.8460.1862120.12342530.12644650.980.9921000.124
5.846-6.750.2112000.14537610.14839610.9740.9881000.15
6.75-8.2650.1981700.13832160.1433860.9720.9891000.15
8.265-11.6840.1531450.13225260.13326710.9840.991000.154
11.684-271.3940.3951010.31514600.31915610.920.9411000.454
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.23540.0190.16181.27380.01120.65280.1186-0.1244-0.05010.2191-0.09170.0120.0606-0.0147-0.02690.1938-0.03840.0530.1609-0.04080.0372-13.7808-60.1105-16.7001
20.9162-0.18750.02410.91790.01381.023-0.0063-0.02230.05940.01650.0327-0.1613-0.15780.0487-0.02640.1337-0.06550.01450.0354-0.01160.161328.0896-41.85-52.6033
31.35410.11150.16540.88170.2450.62310.03140.26070.3482-0.09250.0295-0.1052-0.09840.0042-0.06090.3232-0.00410.0750.27690.09720.12822.0692-61.4993-110.8556
40.94670.1043-0.05970.9519-0.0631.2577-0.02240.11280.2008-0.10420.0630.1148-0.137-0.0114-0.04060.11760.04750.03480.05060.05760.1132-27.3299-41.9166-79.5504
Refinement TLS groupSelection: ALL

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