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- PDB-4x96: Low resolution crystal structure of Lecithin:Cholesterol Acyltran... -

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Basic information

Entry
Database: PDB / ID: 4x96
TitleLow resolution crystal structure of Lecithin:Cholesterol Acyltransferase (LCAT; residues 21-397)
ComponentsPhosphatidylcholine-sterol acyltransferase
KeywordsTRANSFERASE / hydrolase / phospholipase / esterase / acyltransferase
Function / homology
Function and homology information


phosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / regulation of high-density lipoprotein particle assembly / platelet-activating factor acetyltransferase activity / sterol ester esterase activity / 1-alkyl-2-acetylglycerophosphocholine esterase / 1-alkyl-2-acetylglycerophosphocholine esterase activity / apolipoprotein A-I binding / phosphatidylcholine metabolic process / phosphatidylcholine biosynthetic process ...phosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / regulation of high-density lipoprotein particle assembly / platelet-activating factor acetyltransferase activity / sterol ester esterase activity / 1-alkyl-2-acetylglycerophosphocholine esterase / 1-alkyl-2-acetylglycerophosphocholine esterase activity / apolipoprotein A-I binding / phosphatidylcholine metabolic process / phosphatidylcholine biosynthetic process / very-low-density lipoprotein particle remodeling / high-density lipoprotein particle remodeling / reverse cholesterol transport / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / HDL remodeling / phospholipid metabolic process / cholesterol metabolic process / cholesterol homeostasis / lipid metabolic process / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Phosphatidylcholine-sterol acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.69 Å
AuthorsGlukhova, A. / Tesmer, J.J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase.
Authors: Glukhova, A. / Hinkovska-Galcheva, V. / Kelly, R. / Abe, A. / Shayman, J.A. / Tesmer, J.J.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Phosphatidylcholine-sterol acyltransferase
A: Phosphatidylcholine-sterol acyltransferase
B: Phosphatidylcholine-sterol acyltransferase
C: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,34016
Polymers174,7634
Non-polymers5,57712
Water00
1
A: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0854
Polymers43,6911
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0854
Polymers43,6911
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0854
Polymers43,6911
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0854
Polymers43,6911
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)367.258, 367.258, 187.069
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 22 - 396 / Label seq-ID: 2 - 376

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11DA
21AB
12DA
22BC
13DA
23CD
14AB
24BC
15AB
25CD
16BC
26CD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Phosphatidylcholine-sterol acyltransferase / Lecithin-cholesterol acyltransferase / Phospholipid-cholesterol acyltransferase


Mass: 43690.727 Da / Num. of mol.: 4 / Fragment: UNP residues 45-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCAT / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P04180, phosphatidylcholine-sterol O-acyltransferase
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 8 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 13.89 Å3/Da / Density % sol: 87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na acetate pH 5.0, 13% isopropanol, and 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 8.69→30 Å / Num. obs: 7324 / % possible obs: 98.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.093 / Rrim(I) all: 0.21 / Χ2: 0.972 / Net I/av σ(I): 8.233 / Net I/σ(I): 3.3 / Num. measured all: 37449
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.7-8.854.80.5293650.7940.2640.5920.28194.8
8.85-950.4993420.7930.2470.5570.33796.6
9-9.174.90.3973650.8980.1960.4430.36796.6
9.17-9.3550.3453620.8530.1730.3880.37795.8
9.35-9.5550.373560.8870.1830.4140.44197.5
9.55-9.764.90.3113550.910.1540.3480.45797.3
9.76-105.10.3023720.9210.1480.3370.53699.5
10-10.2650.2743720.920.1350.3060.57199.5
10.26-10.555.20.2513690.9290.1230.2790.65599.2
10.55-10.875.20.2283630.9560.1120.2550.819100
10.87-11.245.30.2173710.9590.1050.2421.029100
11.24-11.675.40.1923820.9640.0920.2131.078100
11.67-12.165.40.1873640.9670.0890.2071.313100
12.16-12.765.50.1753690.9640.0830.1941.147100
12.76-13.495.50.1863640.9590.0880.2061.406100
13.49-14.425.50.173760.9670.080.1881.384100
14.42-15.685.50.1573770.980.0740.1731.382100
15.68-17.545.40.1423600.9860.0670.1571.611100
17.54-20.85.10.1283730.9810.0630.1432.106100
20.8-303.50.0933670.9870.0560.1092.11798.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X90

4x90


Resolution: 8.69→30 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.837 / SU B: 733.098 / SU ML: 2.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 2.754 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 367 5 %RANDOM
Rwork0.2096 ---
obs0.2105 6954 94.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 575.19 Å2 / Biso mean: 359.555 Å2 / Biso min: 194.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å2-0.96 Å20 Å2
2---1.92 Å20 Å2
3---6.22 Å2
Refinement stepCycle: final / Resolution: 8.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12044 0 368 0 12412
Biso mean--444.21 --
Num. residues----1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912824
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211816
X-RAY DIFFRACTIONr_angle_refined_deg1.171.98817540
X-RAY DIFFRACTIONr_angle_other_deg0.866327068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72951496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35923.379580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.454151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7621576
X-RAY DIFFRACTIONr_chiral_restr0.0860.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114160
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023032
X-RAY DIFFRACTIONr_mcbond_it6.93830.9275996
X-RAY DIFFRACTIONr_mcbond_other6.93730.9275995
X-RAY DIFFRACTIONr_mcangle_it12.79146.3847488
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D219530.04
12A219530.04
21D219420.04
22B219420.04
31D218930.05
32C218930.05
41A221120.02
42B221120.02
51A220720.04
52C220720.04
61B220520.04
62C220520.04
LS refinement shellResolution: 8.691→8.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 26 -
Rwork0.302 332 -
all-358 -
obs--66.42 %
Refinement TLS params.

Method: refined / 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)
12.0164-0.83740.56132.18671.99333.05470.8788-0.3205-0.2673-0.6302-0.362-0.4175-0.1705-0.3598-0.51680.4864-0.2164-0.08380.70070.54270.6082386.344759.7561-71.0904
20.9172-0.94821.25563.5983-0.05792.51280.3098-0.0712-0.1083-0.602-0.510.1860.1409-0.18530.20020.3095-0.0974-0.08820.33340.24230.6111382.684321.9454-95.1927
31.998-1.2969-0.37473.3797-2.142.34480.3029-0.1108-0.3299-0.0620.06910.5596-0.25630.0792-0.3720.3445-0.06320.01420.5947-0.15810.4234411.727592.7201-50.1267
43.6181.0941-1.30182.2189-0.55341.14260.1507-0.63860.2419-0.4321-0.3269-0.02530.22770.05590.17620.42690.12630.04030.5477-0.15390.1566395.9484100.2498-92.3567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D22 - 471
2X-RAY DIFFRACTION2A22 - 471
3X-RAY DIFFRACTION3B22 - 471
4X-RAY DIFFRACTION4C22 - 471

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