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- PDB-6znw: Methanosaeta concilii ATP citrate lyase (D541A mutant) in complex... -

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Basic information

Entry
Database: PDB / ID: 6znw
TitleMethanosaeta concilii ATP citrate lyase (D541A mutant) in complex with (3S)-citryl-CoA.
Components
  • Citrate lyase, subunit 1
  • Methanosaeta concilii ACLY-B
KeywordsLYASE / acetyl-CoA production / metabolism / atp citrate lyase / lipogenesis
Function / homology
Function and homology information


succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / ATP citrate synthase / ATP citrate synthase activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / lipid metabolic process / lyase activity / ATP binding
Similarity search - Function
: / ATP-citrate synthase ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / Succinyl-CoA synthetase-like
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / (3S)-citryl-Coenzyme A / ATP citrate synthase
Similarity search - Component
Biological speciesMethanothrix soehngenii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.121 Å
AuthorsVerschueren, K.H.G. / Verstraete, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0619N Belgium
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2021
Title: Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.
Authors: Verstraete, K. / Verschueren, K.H.G. / Dansercoer, A. / Savvides, S.N.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 25, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Citrate lyase, subunit 1
B: Methanosaeta concilii ACLY-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7066
Polymers116,4562
Non-polymers1,2504
Water5,260292
1
A: Citrate lyase, subunit 1
B: Methanosaeta concilii ACLY-B
hetero molecules

A: Citrate lyase, subunit 1
B: Methanosaeta concilii ACLY-B
hetero molecules

A: Citrate lyase, subunit 1
B: Methanosaeta concilii ACLY-B
hetero molecules

A: Citrate lyase, subunit 1
B: Methanosaeta concilii ACLY-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,82424
Polymers465,8248
Non-polymers5,00016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area54070 Å2
ΔGint-339 kcal/mol
Surface area153940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.531, 154.373, 276.054
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-981-

HOH

21B-1049-

HOH

31B-1053-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Citrate lyase, subunit 1


Mass: 47307.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothrix soehngenii (archaea) / Gene: ACLY-A / Plasmid: pET11a-ACLY-A/B / Details (production host): Bicistronic construct / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W8FB26, ATP citrate synthase
#2: Protein Methanosaeta concilii ACLY-B


Mass: 69148.570 Da / Num. of mol.: 1 / Mutation: Asp541Ala
Source method: isolated from a genetically manipulated source
Details: M. concilii ACLY-B fused to a C-terminal hexahistidine tag
Source: (gene. exp.) Methanothrix soehngenii (archaea) / Gene: ACLY-B / Plasmid: pET11a-ACLY-A/B / Details (production host): Bicistronic construct / Production host: Escherichia coli BL21(DE3) (bacteria) / References: ATP citrate synthase

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Non-polymers , 5 types, 296 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-Q5B / (3S)-citryl-Coenzyme A / (2~{S})-2-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid


Mass: 941.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42N7O22P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M xylitol 0.02 M myo-inositol 0.02 M D-(-)-fructose 0.02 M L-rhamnose monohydrate 0.02 M D-sorbitol 0.1 M BES/Triethanolamine pH 7.5 12.5 % PEG4000 20 % 1,2,6-hexanetriol
Temp details: Temperature controlled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976245 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2020 / Details: Toroidal mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976245 Å / Relative weight: 1
ReflectionResolution: 2.12→139 Å / Num. obs: 88579 / % possible obs: 99.2 % / Redundancy: 13.6 % / Biso Wilson estimate: 44.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0107 / Net I/σ(I): 18.58
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 13824 / CC1/2: 0.511 / Rrim(I) all: 2.596 / % possible all: 96.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20200131data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hxi

6hxi


Resolution: 2.121→79.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 4490 -RANDOM
Rwork0.1857 ---
obs0.1866 88580 99.2 %-
Displacement parametersBiso mean: 103.91 Å2
Baniso -1Baniso -2Baniso -3
1-4.4514 Å20 Å20 Å2
2--1.7136 Å20 Å2
3----6.165 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.121→79.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7909 0 79 292 8280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088160HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9311049HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2868SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1390HARMONIC5
X-RAY DIFFRACTIONt_it8155HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1068SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle8HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact5958SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.08
LS refinement shellResolution: 2.121→2.14 Å
RfactorNum. reflection% reflection
Rfree0.2526 92 -
Rwork0.2261 --
obs--88.42 %
Refinement TLS params.

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)
19.0798.5903-1.386320.4365-9.214311.1867-0.28020.2503-1.19530.25030.55211.298-1.19531.298-0.2719-0.0742-0.53850.1412-0.5833-0.10310.86323.102155.610333.6224
29.0145-5.0002-0.22353.8113-3.28265.81760.4828-1.0495-1.0714-1.0495-0.36911.2376-1.07141.2376-0.1137-0.2978-0.75990.0056-0.6965-0.06710.786333.729861.469131.2083
35.5463-0.00370.84910.89470.4461.4781-0.40430.2804-1.09660.28040.37110.6983-1.09660.69830.03320.1019-0.5469-0.0472-0.8536-0.21461.319622.44864.438141.9239
46.38461.0911-1.413913.661-2.81634.6853-0.3460.0658-1.12930.06580.48750.6391-1.12930.6391-0.1415-0.0138-0.4983-0.0742-0.69060.09961.287517.25157.822435.4295
512.2021-1.69080.239225.94884.527300.01390.4568-0.78260.45680.47191.6212-0.78261.6212-0.4858-0.2621-0.51850.2027-0.3541-0.36420.214129.109842.881238.963
65.45722.0631-0.12015.66710.18362.4375-0.13370.7520.28490.7520.50820.79690.28490.7969-0.37450.1289-0.0035-0.2361-0.1092-0.49470.189823.180522.500348.3192
714.23912.45763.977510.30440.8235.08380.49651.85250.90021.8525-0.12191.21320.90021.2132-0.37460.63420.0413-0.536-0.2871-0.1993-0.147720.189414.155957.8079
84.2552.12880.69038.19083.02982.0889-0.25250.0937-0.53310.09370.0741-0.197-0.5331-0.1970.17840.0279-0.10190.0645-0.16640.04250.2549-7.284529.502135.3193
93.235-0.23950.0674.06231.36073.1643-0.15241.0901-0.25511.09010.2829-0.0886-0.2551-0.0886-0.13060.3846-0.03870.1356-0.344-0.30370.0279-0.794434.419354.61
102.4967-0.1453-0.47385.99342.98063.78740.04481.99860.28131.99860.27970.11340.28130.1134-0.32450.54120.0536-0.0543-0.2579-0.2698-0.23722.515929.011960.4445
111.1877-0.0038-0.27710.90850.08651.67830.13750.00950.09280.0095-0.03850.50970.09280.5097-0.099-0.23560.006-0.01710.1607-0.01290.045316.3992-2.98785.5204
121.8202-0.15410.01180.6271-0.13111.99990.1234-0.09350.4718-0.0935-0.0710.35610.47180.3561-0.0525-0.11490.1326-0.03410.0717-0.09870.07912.0752-15.6598-10.4417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|20 }A2 - 20
2X-RAY DIFFRACTION2{ A|21 - A|65 }A21 - 64
3X-RAY DIFFRACTION3{ A|72 - A|186 }A72 - 186
4X-RAY DIFFRACTION4{ A|187 - A|230 }A187 - 230
5X-RAY DIFFRACTION5{ A|231 - A|248 }A231 - 248
6X-RAY DIFFRACTION6{ A|249 - A|388 }A249 - 388
7X-RAY DIFFRACTION7{ A|389 - A|419 }A389 - 419
8X-RAY DIFFRACTION8{ B|4 - B|126 }B4 - 126
9X-RAY DIFFRACTION9{ B|127 - B|270 }B127 - 270
10X-RAY DIFFRACTION10{ B|271 - B|346 }B271 - 346
11X-RAY DIFFRACTION11{ B|347 - B|450 }B347 - 450
12X-RAY DIFFRACTION12{ B|451 - B|701 }B451 - 619
13X-RAY DIFFRACTION12{ B|451 - B|701 }B701

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