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- PDB-2xkl: Crystal Structure of Mouse Apolipoprotein M -

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Basic information

Entry
Database: PDB / ID: 2xkl
TitleCrystal Structure of Mouse Apolipoprotein M
ComponentsAPOLIPOPROTEIN M
KeywordsLIPID TRANSPORT
Function / homology
Function and homology information


negative regulation of plasma lipoprotein oxidation / Retinoid metabolism and transport / 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 ...negative regulation of plasma lipoprotein oxidation / Retinoid metabolism and transport / 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 / phospholipid binding / extracellular space / extracellular region
Similarity search - Function
Apolipoprotein M / ApoM domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-PROPANOL / Apolipoprotein M
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSevvana, M. / Kassler, K. / Josefin, A. / Weiler, S. / Dahlback, B. / Sticht, H. / Muller, Y.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Mouse Apom Displays an Unprecedented Seven-Stranded Lipocalin Fold: Folding Decoy or Alternative Native Fold?
Authors: Sevvana, M. / Kassler, K. / Ahnstrom, J. / Weiler, S. / Dahlback, B. / Sticht, H. / Muller, Y.A.
History
DepositionJul 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet / 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 / _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_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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
A: APOLIPOPROTEIN M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3395
Polymers19,1021
Non-polymers2374
Water1,67593
1
A: APOLIPOPROTEIN M
hetero molecules

A: APOLIPOPROTEIN M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,67810
Polymers38,2032
Non-polymers4748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area2930 Å2
ΔGint-21.2 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.930, 53.930, 207.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 19101.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z1R3

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 46.02 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M NA CITRATE PH 5.6, 20% V/V 2-PROPANOL, 20% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Type: BESSY / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 6802 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 26.489 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.84
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 8.08 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.56 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WEW

2wew


Resolution: 2.5→19.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.88 / SU B: 16.247 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 340 5 %RANDOM
Rwork0.18731 ---
obs0.19033 6450 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.46 Å20 Å2
2--0.91 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 15 93 1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9731632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81923.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90515192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.219158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02910
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2527
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2791
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.5747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10421207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7423472
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9894.5425
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 24 -
Rwork0.209 449 -
obs--100 %
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)
14.4076-0.0835-0.43490.42760.69851.16160.13430.2099-0.0411-0.0287-0.25030.2192-0.0656-0.02650.1160.03840.0343-0.00920.04280.0160.032514.402520.7279101.0769
24.0656-1.1318-1.09332.95351.14813.33020.0309-0.00580.1793-0.0923-0.0599-0.0414-0.23920.16090.029-0.0016-0.0391-0.01090.0296-0.01360.011622.977120.0007106.0583
36.40732.0046-1.9352.988-0.29313.8648-0.25730.2482-0.4075-0.01030.02390.14080.28570.07910.23340.0580.02760.02110.0096-0.02830.044717.405514.601298.6
42.32440.0191-1.1521.3981.24286.713-0.23280.0773-0.16990.1392-0.0380.23270.7031-0.12650.27080.07930.00720.0201-0.0257-0.00580.042119.93948.8922101.2737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 54
2X-RAY DIFFRACTION2A55 - 126
3X-RAY DIFFRACTION3A127 - 158
4X-RAY DIFFRACTION4A159 - 189

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