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- PDB-3pff: Truncated human atp-citrate lyase with ADP and tartrate bound -

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Basic information

Entry
Database: PDB / ID: 3pff
TitleTruncated human atp-citrate lyase with ADP and tartrate bound
ComponentsATP-citrate synthase
KeywordsTRANSFERASE / PHOSPHOHISTIDINE / ORGANIC ACID / ATP-GRASP / LYASE
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 / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / 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 / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol 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, 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 synthase / 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 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; 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
ADENOSINE-5'-DIPHOSPHATE / L(+)-TARTARIC ACID / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsFraser, M.E. / Sun, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: ADP-Mg2+ bound to the ATP-grasp domain of ATP-citrate lyase.
Authors: Sun, T. / Hayakawa, K. / Fraser, M.E.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4385
Polymers90,8121
Non-polymers6264
Water7,008389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-citrate synthase
hetero molecules

A: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,87510
Polymers181,6242
Non-polymers1,2528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4430 Å2
ΔGint-63 kcal/mol
Surface area58450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.540, 61.700, 107.980
Angle α, β, γ (deg.)90.00, 125.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1164-

HOH

21A-1216-

HOH

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Components

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


Mass: 90811.812 Da / Num. of mol.: 1 / Fragment: unp residues 1-817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Plasmid: PET42B+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53396, ATP citrate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12.5% polyethylene glycol 3350, 125 mM sodium tartrate, 100 mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 2, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→43.97 Å / Num. all: 39343 / Num. obs: 39343 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.097 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5349 / % possible all: 92.8

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Processing

Software
NameVersionClassification
MxDCdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRIES: 3MWD, 3MWE

3mwd

3mwe


Resolution: 2.3→43.97 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.86 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2256 5.96 %Matching 3MWD/3MWE
Rwork0.1677 ---
all0.1713 37841 --
obs0.1713 37841 94.11 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.878 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.7838 Å20 Å22.0685 Å2
2--2.7386 Å20 Å2
3---8.0452 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 39 389 6116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075855
X-RAY DIFFRACTIONf_angle_d1.0637935
X-RAY DIFFRACTIONf_dihedral_angle_d13.1382150
X-RAY DIFFRACTIONf_chiral_restr0.068890
X-RAY DIFFRACTIONf_plane_restr0.0041012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.2554850.2121798X-RAY DIFFRACTION75
2.35-2.40470.31191070.22082107X-RAY DIFFRACTION90
2.4047-2.46480.28911060.21382109X-RAY DIFFRACTION89
2.4648-2.53150.28221320.20442142X-RAY DIFFRACTION91
2.5315-2.6060.2841450.19952117X-RAY DIFFRACTION91
2.606-2.69010.2671470.1912174X-RAY DIFFRACTION93
2.6901-2.78620.2471590.18262230X-RAY DIFFRACTION95
2.7862-2.89770.26781350.18272236X-RAY DIFFRACTION95
2.8977-3.02960.23161550.16862263X-RAY DIFFRACTION97
3.0296-3.18930.23411550.16322281X-RAY DIFFRACTION97
3.1893-3.3890.22061480.16222314X-RAY DIFFRACTION98
3.389-3.65060.20031550.15472308X-RAY DIFFRACTION98
3.6506-4.01770.20151520.14652348X-RAY DIFFRACTION99
4.0177-4.59850.1831560.13792346X-RAY DIFFRACTION99
4.5985-5.79160.21191560.1512364X-RAY DIFFRACTION99
5.7916-43.97850.22841630.17482448X-RAY DIFFRACTION99

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