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- PDB-8rpl: AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium wi... -

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Basic information

Entry
Database: PDB / ID: 8rpl
TitleAMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP
ComponentsAcetate--CoA ligase
KeywordsLIGASE / Acetate / Acetyl-AMP / CoA / phospho histidine / AcsA
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / cytosol
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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Chem-6R9 / acetate--CoA ligase
Similarity search - Component
Biological speciesChloroflexota bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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)299,07216
Polymers296,4664
Non-polymers2,60612
Water3,261181
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)224,30512
Polymers222,3503
Non-polymers1,9569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
B: Acetate--CoA ligase
C: Acetate--CoA ligase
D: Acetate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,30412
Polymers222,3503
Non-polymers1,9549
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.909, 161.909, 817.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 193 molecules

#2: Chemical
ChemComp-6R9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate


Mass: 389.258 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4 Å3/Da / Density % sol: 64.62 % / Description: trigonal bipyramids
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 uL (protein in 50 mM HEPES pH 7.5, 100 mM KCl) + 2 uL (25% PEG 400, 0.1 M Na-MES, pH 6.5, 0.05 M MnCl2 or MgCl2)

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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 5, 2023 / Details: Si111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 167479 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Biso Wilson estimate: 70 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.146 / Rsym value: 0.142 / Net I/σ(I): 16
Reflection shellResolution: 2.37→2.56 Å / Redundancy: 21.6 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 34212 / CC1/2: 0.502 / Rrim(I) all: 2.97 / Rsym value: 2.9 / % possible all: 100

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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: 2.37→48.304 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.149 / SU B: 16.314 / SU ML: 0.163 / Average fsc free: 0.9592 / Average fsc work: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2007 8378 5.006 %
Rwork0.1613 158976 -
all0.163 --
obs-167354 99.868 %
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: 76.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.658 Å20.329 Å2-0 Å2
2--0.658 Å2-0 Å2
3----2.134 Å2
Refinement stepCycle: LAST / Resolution: 2.37→48.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19931 0 168 181 20280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01220968
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619589
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.83328582
X-RAY DIFFRACTIONr_angle_other_deg0.5711.75645285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04652566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.9465144
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg9.47208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.905103410
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.33810913
X-RAY DIFFRACTIONr_chiral_restr0.0790.23081
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024740
X-RAY DIFFRACTIONr_nbd_refined0.2090.23503
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.217016
X-RAY DIFFRACTIONr_nbtor_refined0.1820.210025
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.210445
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2410
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.23
X-RAY DIFFRACTIONr_metal_ion_refined0.260.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.214
X-RAY DIFFRACTIONr_nbd_other0.2060.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0890.28
X-RAY DIFFRACTIONr_mcbond_it3.7484.96910159
X-RAY DIFFRACTIONr_mcbond_other3.7454.96910159
X-RAY DIFFRACTIONr_mcangle_it5.3128.9412709
X-RAY DIFFRACTIONr_mcangle_other5.3128.94112710
X-RAY DIFFRACTIONr_scbond_it5.0925.46210809
X-RAY DIFFRACTIONr_scbond_other5.0915.46210807
X-RAY DIFFRACTIONr_scangle_it7.5119.79815856
X-RAY DIFFRACTIONr_scangle_other7.5119.79915857
X-RAY DIFFRACTIONr_lrange_it9.0146.30122156
X-RAY DIFFRACTIONr_lrange_other9.0146.15922140
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
2.37-2.4310.3315900.327114940.327122290.9070.91398.81430.33
2.431-2.4980.3455980.313113310.314119540.9190.93299.79090.314
2.498-2.570.3166140.286110710.288116880.9360.9599.97430.284
2.57-2.6490.2995550.264107070.266112640.9460.95999.98220.257
2.649-2.7360.2815590.238103650.24109240.9570.9691000.226
2.736-2.8310.2495440.216100660.218106140.9630.97599.96230.198
2.831-2.9380.245030.19997290.201102330.9650.97899.99020.179
2.938-3.0570.2414400.18894500.1998910.9640.97999.98990.168
3.057-3.1930.2364840.18689720.18994570.9650.97999.98940.167
3.193-3.3480.2234530.17586040.17790570.9670.9821000.16
3.348-3.5280.2144330.17782120.17986470.9720.98299.97690.165
3.528-3.7410.1994430.16377520.16681950.9790.9861000.154
3.741-3.9970.1843840.14273240.14477080.980.9891000.136
3.997-4.3150.1633460.12868430.12971890.9840.9911000.125
4.315-4.7230.1423540.11363180.11566720.9880.9931000.113
4.723-5.2740.1523010.10657300.10960310.9880.9931000.107
5.274-6.0780.1812720.13150930.13353650.9840.9911000.131
6.078-7.4150.1732290.13343670.13545970.9810.9999.97820.135
7.415-10.3650.1681690.1334570.13236260.9820.991000.138
10.365-48.3040.2641070.21220910.21522020.940.9799.81840.229
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.134-0.00580.07671.29150.04421.0981-0.01460.0929-0.0419-0.01030.0336-0.0450.0090.0343-0.0190.0510.02150.01930.04980.04570.06959.313-18.030516.6639
21.0219-0.0906-0.11311.25120.17141.37320.0374-0.0782-0.14510.0487-0.04060.0875-0.042-0.24530.00320.00970.01540.02720.23540.01940.230122.2511-45.622252.5099
31.2077-0.0327-0.04871.0250.17481.55090.0217-0.10370.08540.02710.04920.0089-0.1611-0.1151-0.07090.21960.11240.04710.07130.00810.159250.37682.951779.3279
40.98960.23880.28621.6932-0.03630.5910.041-0.04130.09630.3674-0.01250.4198-0.0822-0.2479-0.02850.46060.02010.17550.35380.00430.22442.593-49.8141111.1104
Refinement TLS groupSelection: ALL

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