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- PDB-2wew: Crystal structure of human apoM in complex with myristic acid -

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Basic information

Entry
Database: PDB / ID: 2wew
TitleCrystal structure of human apoM in complex with myristic acid
ComponentsAPOLIPOPROTEIN M
KeywordsLIPID TRANSPORT / LIGAND-BINDING SPECIFICITY / GLYCOPROTEIN / MYRISTIC ACID / HDL / LIPOCALIN / TRANSPORT / LIPOPROTEINS
Function / homology
Function and homology information


negative regulation of plasma lipoprotein oxidation / spherical high-density lipoprotein particle / discoidal high-density lipoprotein particle / lipoprotein metabolic process / high-density lipoprotein particle clearance / lipid transporter activity / high-density lipoprotein particle remodeling / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle ...negative regulation of plasma lipoprotein oxidation / spherical high-density lipoprotein particle / discoidal high-density lipoprotein particle / lipoprotein metabolic process / high-density lipoprotein particle clearance / lipid transporter activity / high-density lipoprotein particle remodeling / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / low-density lipoprotein particle / high-density lipoprotein particle / cholesterol efflux / antioxidant activity / Retinoid metabolism and transport / cholesterol homeostasis / phospholipid binding / extracellular region
Similarity search - Function
Apolipoprotein M / ApoM domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Apolipoprotein M
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsSevvana, M. / Ahnstrom, J. / Egerer-Sieber, C. / Dahlback, B. / Muller, Y.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Serendipitous Fatty Acid Binding Reveals the Structural Determinants for Ligand Recognition in Apolipoprotein M.
Authors: Sevvana, M. / Ahnstrom, J. / Egerer-Sieber, C. / Lange, H.A. / Dahlback, B. / Muller, Y.A.
History
DepositionApr 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5333
Polymers19,2431
Non-polymers2902
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.940, 49.940, 144.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein APOLIPOPROTEIN M / PROTEIN G3A / APO-M / APOM


Mass: 19242.789 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95445
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 22-188 WITHOUT SIGNAL PEPTIDE HAVE BEEN CLONED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 % / Description: NONE
Crystal growpH: 7.2
Details: ABOUT 1-2 MICROL OF PROTEIN (10-16 MG/ML IN 20 MM TRIS-HCL, PH 7.2) WERE MIXED WITH 1-2 MICROL OF 30 % PEG1500 (W/V, IN DEIONISED WATER) AND EQUILIBRATED AGAINST 700 MICROL OF RESERVOIR ...Details: ABOUT 1-2 MICROL OF PROTEIN (10-16 MG/ML IN 20 MM TRIS-HCL, PH 7.2) WERE MIXED WITH 1-2 MICROL OF 30 % PEG1500 (W/V, IN DEIONISED WATER) AND EQUILIBRATED AGAINST 700 MICROL OF RESERVOIR SOLUTION CONTAINING 30 % PEG1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: RAYONICS / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 13952 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 7.06 % / Biso Wilson estimate: 36.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.18
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.84 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.076 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26746 696 5 %RANDOM
Rwork0.20813 ---
obs0.21112 13253 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---1.49 Å20 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 20 83 1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9731906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89124.28663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31915235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.361158
X-RAY DIFFRACTIONr_chiral_restr0.1230.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.2525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2921
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.5900
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45621404
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3473581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2974.5502
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 42 -
Rwork0.223 870 -
obs--89.41 %
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)
114.38113.7233.02431.15881.08042.3956-0.02910.9736-1.23950.13080.1326-0.34170.25040.3611-0.10350.16010.13170.00380.199-0.14690.198125.1203-10.769425.4068
23.52120.8356-0.41322.55540.06630.1594-0.02880.30890.143-0.4975-0.0257-0.19670.0043-0.04010.05450.1810.05330.03190.12760.03130.074810.66412.058327.4671
33.10551.22851.24237.90093.22353.13670.03690.40860.0589-0.59860.0427-0.1069-0.1127-0.0895-0.07960.16570.0594-0.03110.09210.01260.02132.30817.122727.4722
41.2237-1.8654-1.323615.38239.98957.0230.06750.36820.1971-1.01070.0088-0.107-0.52470.0011-0.07640.25990.0782-0.02560.13680.0069-0.00452.6914.308121.1539
58.9729-0.71510.86413.80031.10813.08420.13551.10550.223-0.7249-0.037-0.0366-0.61480.596-0.09850.13550.05630.04220.17120.0298-0.007712.1816-0.72219.4478
65.7753-0.4032-1.15491.73310.77053.55260.00830.16530.2799-0.19590.0287-0.3776-0.06850.167-0.0370.05770.04690.02130.05190.02540.139317.79822.243931.1834
75.4258-3.3978-1.79113.81982.46463.8980.0377-0.07480.4924-0.04190.0374-0.2586-0.07180.0867-0.07510.0590.0064-0.0125-0.01150.06080.107411.53139.537133.9785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 35
2X-RAY DIFFRACTION2A36 - 63
3X-RAY DIFFRACTION3A64 - 92
4X-RAY DIFFRACTION4A93 - 108
5X-RAY DIFFRACTION5A109 - 129
6X-RAY DIFFRACTION6A130 - 167
7X-RAY DIFFRACTION7A168 - 187

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