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- PDB-4xx1: Low resolution structure of LCAT in complex with Fab1 -

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Basic information

Entry
Database: PDB / ID: 4xx1
TitleLow resolution structure of LCAT in complex with Fab1
Components
  • Fab1 heavy chain
  • Fab1 light chain
  • Phosphatidylcholine-sterol acyltransferase
KeywordsHydrolase/Immune system / a/b Hydrolase / Complex / Hydrolase-Immune system complex
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 / phospholipase A2 activity / phosphatidylcholine metabolic 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 / phospholipase A2 activity / phosphatidylcholine metabolic process / phosphatidylcholine biosynthetic process / aflatoxin metabolic 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 / response to copper ion / cholesterol metabolic process / phospholipid metabolic process / response to glucocorticoid / 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, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich ...Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphatidylcholine-sterol acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPiper, D.E. / Walker, N.P.C. / Romanow, W.G. / Thibault, S.T.
CitationJournal: J.Lipid Res. / Year: 2015
Title: The high-resolution crystal structure of human LCAT.
Authors: Piper, D.E. / Romanow, W.G. / Gunawardane, R.N. / Fordstrom, P. / Masterman, S. / Pan, O. / Thibault, S.T. / Zhang, R. / Meininger, D. / Schwarz, M. / Wang, Z. / King, C. / Zhou, M. / Walker, N.P.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 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
L: Fab1 light chain
H: Fab1 heavy chain
A: Phosphatidylcholine-sterol acyltransferase
G: Fab1 light chain
E: Fab1 heavy chain
B: Phosphatidylcholine-sterol acyltransferase
O: Fab1 light chain
M: Fab1 heavy chain
J: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,92818
Polymers288,9379
Non-polymers1,9919
Water00
1
L: Fab1 light chain
H: Fab1 heavy chain
A: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9766
Polymers96,3123
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-32 kcal/mol
Surface area34700 Å2
MethodPISA
2
G: Fab1 light chain
E: Fab1 heavy chain
B: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9766
Polymers96,3123
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-28 kcal/mol
Surface area34520 Å2
MethodPISA
3
O: Fab1 light chain
M: Fab1 heavy chain
J: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9766
Polymers96,3123
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-18 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.419, 166.419, 97.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody Fab1 light chain


Mass: 22744.133 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab1 heavy chain


Mass: 25644.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Phosphatidylcholine-sterol acyltransferase / Lecithin-cholesterol acyltransferase / Phospholipid-cholesterol acyltransferase


Mass: 47923.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCAT / Production host: Homo sapiens (human)
References: UniProt: P04180, phosphatidylcholine-sterol O-acyltransferase
#4: 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.: 9 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium tartrate, 0.001 M zinc acetate, 13% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.2499 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2499 Å / Relative weight: 1
ReflectionResolution: 3.6→144.123 Å / Num. all: 34818 / Num. obs: 34818 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 121.61 Å2 / Rpim(I) all: 0.078 / Rrim(I) all: 0.182 / Rsym value: 0.164 / Net I/av σ(I): 2.711 / Net I/σ(I): 7 / Num. measured all: 189720
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.6-3.794.90.9060.82498250830.4510.9062.199
3.79-4.025.30.5981.22551948030.2860.5983.199.3
4.02-4.35.50.3691.92495245030.1730.3694.899.1
4.3-4.655.60.2332.92339241970.1090.233799.3
4.65-5.095.60.1873.42184539000.0880.187899.6
5.09-5.695.60.1534.11960935050.0720.1538.999.5
5.69-6.575.60.1324.81730330860.0610.1329.599.5
6.57-8.055.60.1055.11477726370.0490.10511.299.8
8.05-11.385.60.0915.41121819940.0430.09114.199.5
11.38-80.8475.50.1054.9612311100.050.10514.799.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XWG

4xwg


Resolution: 3.6→72.062 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1750 5.03 %Random Selection
Rwork0.1957 33056 --
obs0.1998 34806 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.36 Å2 / Biso mean: 127.0908 Å2 / Biso min: 58.67 Å2
Refinement stepCycle: final / Resolution: 3.6→72.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17112 0 126 0 17238
Biso mean--155.02 --
Num. residues----2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517757
X-RAY DIFFRACTIONf_angle_d0.99224204
X-RAY DIFFRACTIONf_chiral_restr0.0382636
X-RAY DIFFRACTIONf_plane_restr0.0053097
X-RAY DIFFRACTIONf_dihedral_angle_d15.8246298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6002-3.69760.31291380.25372548268699
3.6976-3.80640.3611260.25882512263899
3.8064-3.92920.31981320.24962536266899
3.9292-4.06960.3051390.22722560269999
4.0696-4.23260.26241490.21725292678100
4.2326-4.42520.29461230.20352543266699
4.4252-4.65840.28621400.192530267099
4.6584-4.95020.26221440.192325652709100
4.9502-5.33230.26011240.180625472671100
5.3323-5.86870.29951190.19922560267999
5.8687-6.71740.32081500.204125272677100
6.7174-8.46120.26861450.190225472692100
8.4612-72.07590.23651210.15952552267399

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