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- PDB-5te1: C20S, C293G Mutant N-terminal Human ATP Citrate Lyase Bound to 4R... -

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Basic information

Entry
Database: PDB / ID: 5te1
TitleC20S, C293G Mutant N-terminal Human ATP Citrate Lyase Bound to 4R-Hydroxycitrate
ComponentsATP-citrate synthase
KeywordsTRANSFERASE / ATP grasp domain / 4R hydroxycitrate
Function / homology
Function and homology information


ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / acetyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / coenzyme A metabolic process / oxaloacetate metabolic process / negative regulation of ferroptosis / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / acetyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / coenzyme A metabolic process / oxaloacetate metabolic process / negative regulation of ferroptosis / cholesterol biosynthetic process / lipid biosynthetic process / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / ciliary basal body / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
ATP-citrate synthase / : / ATP-citrate synthase ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. ...ATP-citrate synthase / : / ATP-citrate synthase ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-C-carboxy-2-deoxy-L-threo-pentaric acid / PHOSPHATE ION / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsHu, J. / Fraser, M.E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Binding of hydroxycitrate to human ATP-citrate lyase.
Authors: Hu, J. / Komakula, A. / Fraser, M.E.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,8758
Polymers181,2232
Non-polymers6526
Water13,511750
1
A: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9384
Polymers90,6121
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9384
Polymers90,6121
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.770, 73.320, 131.370
Angle α, β, γ (deg.)90.00, 97.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / ACL / Citrate cleavage enzyme


Mass: 90611.508 Da / Num. of mol.: 2 / Mutation: C20S, C293G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Production host: Escherichia coli (E. coli) / References: UniProt: P53396, ATP citrate synthase
#2: Chemical ChemComp-7A2 / 3-C-carboxy-2-deoxy-L-threo-pentaric acid


Mass: 208.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O8
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 12.5% P3350, 200 mM MES pH 5.9, 125 mM ammonium acetate pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.25→49.01 Å / Num. obs: 82560 / % possible obs: 93.2 % / Redundancy: 2.8 % / Net I/σ(I): 6.1

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Processing

SoftwareName: PHENIX / Version: (1.10_2152: ???) / Classification: refinement
RefinementResolution: 2.25→49.01 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.11
RfactorNum. reflection% reflection
Rfree0.247 4131 5.01 %
Rwork0.1881 --
obs0.1911 82521 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11484 0 40 750 12274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311770
X-RAY DIFFRACTIONf_angle_d1.17615941
X-RAY DIFFRACTIONf_dihedral_angle_d12.9647001
X-RAY DIFFRACTIONf_chiral_restr0.0631781
X-RAY DIFFRACTIONf_plane_restr0.0082042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.31211290.24792688X-RAY DIFFRACTION95
2.2756-2.30240.28341610.22352632X-RAY DIFFRACTION95
2.3024-2.33040.29971510.22362639X-RAY DIFFRACTION95
2.3304-2.35990.25911440.21082673X-RAY DIFFRACTION95
2.3599-2.3910.28981080.20252667X-RAY DIFFRACTION95
2.391-2.42370.29121210.20892673X-RAY DIFFRACTION95
2.4237-2.45840.28741470.20242664X-RAY DIFFRACTION95
2.4584-2.49510.2621380.19822606X-RAY DIFFRACTION95
2.4951-2.5340.27981410.19682677X-RAY DIFFRACTION95
2.534-2.57560.26981420.19662602X-RAY DIFFRACTION94
2.5756-2.620.27841430.19592686X-RAY DIFFRACTION95
2.62-2.66760.27411290.20642625X-RAY DIFFRACTION94
2.6676-2.71890.25611490.20752612X-RAY DIFFRACTION94
2.7189-2.77440.30471390.20262622X-RAY DIFFRACTION94
2.7744-2.83480.26061330.19662633X-RAY DIFFRACTION93
2.8348-2.90070.28611340.18872625X-RAY DIFFRACTION93
2.9007-2.97320.25921480.18592572X-RAY DIFFRACTION93
2.9732-3.05360.25211540.19662638X-RAY DIFFRACTION93
3.0536-3.14340.27391280.18562589X-RAY DIFFRACTION93
3.1434-3.24490.23651290.18662591X-RAY DIFFRACTION93
3.2449-3.36080.24811260.19062618X-RAY DIFFRACTION92
3.3608-3.49540.25391160.192623X-RAY DIFFRACTION92
3.4954-3.65440.23341350.1762588X-RAY DIFFRACTION92
3.6544-3.8470.22811540.15992575X-RAY DIFFRACTION92
3.847-4.08790.21211480.15652550X-RAY DIFFRACTION91
4.0879-4.40330.19921430.15882549X-RAY DIFFRACTION91
4.4033-4.84610.19371470.14912544X-RAY DIFFRACTION90
4.8461-5.54650.21071260.16642561X-RAY DIFFRACTION90
5.5465-6.98480.23231390.20662521X-RAY DIFFRACTION89
6.9848-49.02230.24541290.22542547X-RAY DIFFRACTION86

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