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- PDB-4xwg: Crystal Structure of LCAT (C31Y) in complex with Fab1 -

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Basic information

Entry
Database: PDB / ID: 4xwg
TitleCrystal Structure of LCAT (C31Y) in complex with Fab1
Components
  • Fab1 Heavy Chain
  • Fab1 Light Chain
  • Phosphatidylcholine-sterol acyltransferase
KeywordsHydrolase/Immune system / a-b Hydrolase Complex / esterase / acyl transferase / 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 / apolipoprotein A-I binding / 1-alkyl-2-acetylglycerophosphocholine esterase activity / 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 / apolipoprotein A-I binding / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine metabolic process / phosphatidylcholine biosynthetic process / very-low-density lipoprotein particle remodeling / high-density lipoprotein particle remodeling / reverse cholesterol transport / cholesterol transport / lipoprotein biosynthetic process / 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, 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: 2.65 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 28, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / 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_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,08222
Polymers96,3723
Non-polymers1,71019
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-396 kcal/mol
Surface area34820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.590, 168.590, 93.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab1 Light Chain


Mass: 22744.133 Da / Num. of mol.: 1
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein / Sugars , 2 types, 4 molecules A

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


Mass: 47983.496 Da / Num. of mol.: 1 / Fragment: UNP residues 25-440 / Mutation: C33Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCAT / Production host: Escherichia coli (E. coli)
References: UniProt: P04180, phosphatidylcholine-sterol O-acyltransferase
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / 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

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Non-polymers , 2 types, 120 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.2 M zinc acetate, 0.01 M cobalt chloride, 4-8% PEG 1500
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→84.295 Å / Num. all: 28802 / Num. obs: 28802 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 56.6 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.102 / Rsym value: 0.089 / Net I/av σ(I): 6.588 / Net I/σ(I): 10.3 / Num. measured all: 119076
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
2.65-2.794.10.6441.21710542010.3690.6442.2100
2.79-2.964.10.4081.91638540070.2320.4083.3100
2.96-3.174.10.25831536537250.1460.2584.9100
3.17-3.424.10.1425.41439634750.080.1428.1100
3.42-3.754.20.0878.41338232140.0480.08712100
3.75-4.194.20.06510.61207929000.0360.06515.5100
4.19-4.844.20.0629.91065825550.0340.06218.9100
4.84-5.934.20.0689.3901621530.0370.06819.6100
5.93-8.384.20.04713.3701916750.0260.04720100
8.38-39.394.10.04911.136718970.0280.04923.199

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→34.005 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1414 4.91 %Random selection
Rwork0.1762 27378 --
obs0.1798 28792 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.34 Å2 / Biso mean: 52.2498 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 2.65→34.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 58 104 6398
Biso mean--87.98 46.91 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146506
X-RAY DIFFRACTIONf_angle_d1.548816
X-RAY DIFFRACTIONf_chiral_restr0.065965
X-RAY DIFFRACTIONf_plane_restr0.0081128
X-RAY DIFFRACTIONf_dihedral_angle_d15.7242295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6502-2.74490.31871500.23827402890
2.7449-2.85480.30361250.226927342859
2.8548-2.98460.29931670.217427182885
2.9846-3.14190.30971280.210827422870
3.1419-3.33860.33761340.197527432877
3.3386-3.59610.27851560.180227562912
3.5961-3.95750.24611370.165927222859
3.9575-4.5290.24511430.146727212864
4.529-5.70170.1871310.154527632894
5.7017-34.00790.21861430.173827392882

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