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- PDB-5teq: C20S C293G MUTANT N-TERMINAL HUMAN ATP CITRATE LYASE BOUND TO CITRATE -

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Basic information

Entry
Database: PDB / ID: 5teq
TitleC20S C293G MUTANT N-TERMINAL HUMAN ATP CITRATE LYASE BOUND TO CITRATE
ComponentsATP-citrate synthase
KeywordsTRANSFERASE / ATP-grasp fold / citrate binding
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
D-amino Acid Aminotransferase; Chain A, domain 1 - #110 / 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. ...D-amino Acid Aminotransferase; Chain A, domain 1 - #110 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 22, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)181,8378
Polymers181,2232
Non-polymers6146
Water9,314517
1
A: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9194
Polymers90,6121
Non-polymers3073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9194
Polymers90,6121
Non-polymers3073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.110, 73.100, 131.120
Angle α, β, γ (deg.)90.00, 97.89, 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#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.: 517 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12.5% P3350, 100-200 mM MES pH 7, 125 mM ammonium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97951 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.3→45.08 Å / Num. obs: 79319 / % possible obs: 99.7 % / Redundancy: 3.8 % / Net I/σ(I): 10.6

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Processing

SoftwareName: PHENIX / Version: (1.10_2152: ???) / Classification: refinement
RefinementResolution: 2.3→41.458 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 3988 5.03 %
Rwork0.2017 --
obs0.2039 79291 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11397 0 38 517 11952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211688
X-RAY DIFFRACTIONf_angle_d0.52215834
X-RAY DIFFRACTIONf_dihedral_angle_d10.0886954
X-RAY DIFFRACTIONf_chiral_restr0.0441770
X-RAY DIFFRACTIONf_plane_restr0.0032030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32810.3231570.26492637X-RAY DIFFRACTION100
2.3281-2.35750.29391150.25572725X-RAY DIFFRACTION100
2.3575-2.38850.2951300.26172666X-RAY DIFFRACTION100
2.3885-2.42130.35621470.25442678X-RAY DIFFRACTION100
2.4213-2.45580.341420.25572690X-RAY DIFFRACTION100
2.4558-2.49250.30681390.23922660X-RAY DIFFRACTION100
2.4925-2.53140.29581540.23682664X-RAY DIFFRACTION100
2.5314-2.57290.29741480.23162673X-RAY DIFFRACTION100
2.5729-2.61730.30131340.22962685X-RAY DIFFRACTION100
2.6173-2.66490.28081540.23082648X-RAY DIFFRACTION100
2.6649-2.71610.3121420.22632724X-RAY DIFFRACTION100
2.7161-2.77160.2631210.21122650X-RAY DIFFRACTION100
2.7716-2.83180.27561480.21252706X-RAY DIFFRACTION100
2.8318-2.89770.24811300.20722683X-RAY DIFFRACTION100
2.8977-2.97010.26591640.21132665X-RAY DIFFRACTION100
2.9701-3.05040.25421600.20692670X-RAY DIFFRACTION100
3.0504-3.14010.28041200.20222687X-RAY DIFFRACTION100
3.1401-3.24140.23391420.20732682X-RAY DIFFRACTION100
3.2414-3.35720.2291360.20032699X-RAY DIFFRACTION100
3.3572-3.49160.27391320.20542718X-RAY DIFFRACTION100
3.4916-3.65040.25331290.19882707X-RAY DIFFRACTION99
3.6504-3.84270.24341660.19482645X-RAY DIFFRACTION99
3.8427-4.08330.19931510.17122680X-RAY DIFFRACTION100
4.0833-4.39830.17691530.16112678X-RAY DIFFRACTION100
4.3983-4.84030.21091430.15782732X-RAY DIFFRACTION100
4.8403-5.53930.20451410.17362720X-RAY DIFFRACTION100
5.5393-6.97350.23861490.20892731X-RAY DIFFRACTION100
6.9735-41.46470.20481410.19912800X-RAY DIFFRACTION99

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