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- PDB-6c1z: Crystal structure of Apo Caenorhabditis elegans lipid binding pro... -

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Basic information

Entry
Database: PDB / ID: 6c1z
TitleCrystal structure of Apo Caenorhabditis elegans lipid binding protein 8 (LBP-8)
ComponentsLipid Binding Protein
KeywordsLIPID BINDING PROTEIN / LBP8 / LBP-8 / FABP / fatty acid binding protein / lipid / lipid binding protein 8 / C. elegans / Caenorhabditis elegans / aging / lysosome / lipid transport / monounsaturated fatty acids / fatty acid
Function / homology
Function and homology information


Recycling of bile acids and salts / Triglyceride catabolism / Heme degradation / Signaling by Retinoic Acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / oleic acid binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / lipid transport ...Recycling of bile acids and salts / Triglyceride catabolism / Heme degradation / Signaling by Retinoic Acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / oleic acid binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / lipid transport / long-chain fatty acid transport / fatty acid transport / fatty acid binding / lysosome / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein homolog 8
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTillman, M.C. / Ortlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
W. M. Keck Foundation United States
CitationJournal: Sci Rep / Year: 2019
Title: Structural characterization of life-extending Caenorhabditis elegans Lipid Binding Protein 8.
Authors: Tillman, M.C. / Khadka, M. / Duffy, J. / Wang, M.C. / Ortlund, E.A.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3813
Polymers16,1881
Non-polymers1922
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.904, 41.857, 70.896
Angle α, β, γ (deg.)90.000, 91.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lipid Binding Protein


Mass: 16188.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lbp-8, CELE_T22G5.6, T22G5.6 / Production host: Escherichia coli (E. coli) / References: UniProt: O02324
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 2.81 M ammonium sulfate and 0.25 M potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 688051 / % possible obs: 96.3 % / Redundancy: 6.9 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Χ2: 0.902 / Net I/σ(I): 33.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 4481 / CC1/2: 0.833 / Rpim(I) all: 0.274 / Rrim(I) all: 0.666 / Χ2: 0.444 / % possible all: 67.9

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Processing

Software
NameVersionClassification
PHENIXdev_2621refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WVM

3wvm


Resolution: 1.3→31.227 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.55
RfactorNum. reflection% reflection
Rfree0.2101 1642 5.02 %
Rwork0.1903 --
obs0.1914 32689 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.19 Å2 / Biso mean: 35.016 Å2 / Biso min: 16.53 Å2
Refinement stepCycle: final / Resolution: 1.3→31.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 10 92 1244
Biso mean--37.59 37.28 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081176
X-RAY DIFFRACTIONf_angle_d0.8971582
X-RAY DIFFRACTIONf_chiral_restr0.079169
X-RAY DIFFRACTIONf_plane_restr0.006197
X-RAY DIFFRACTIONf_dihedral_angle_d13.307432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.33820.3015930.27421938203173
1.3382-1.38140.28441300.27622383251389
1.3814-1.43080.32751320.27192628276098
1.4308-1.48810.28931440.241526492793100
1.4881-1.55580.26761420.20726642806100
1.5558-1.63780.23981450.202326522797100
1.6378-1.74040.24211400.204927152855100
1.7404-1.87480.24411450.200326642809100
1.8748-2.06340.18721430.177526802823100
2.0634-2.36190.22431410.180626932834100
2.3619-2.97540.19291430.197427152858100
2.9754-31.23610.19241440.17622666281096
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)
13.72110.73463.68367.15160.64073.93650.02090.5518-0.2959-0.6064-0.15540.5516-0.6146-0.27670.24420.28420.0602-0.05550.2916-0.00380.270516.16837.0533.394
22.00660.8656-0.36525.7256-2.40276.5980.2427-0.4232-0.14010.7239-0.27190.0348-0.3115-0.1232-0.02640.2113-0.0529-0.04970.22890.00020.200414.10130.09227.445
38.2588-2.1109-1.72675.97083.60554.2030.2192-0.15360.51340.37980.259-0.192-0.32171.0726-0.31780.2277-0.0678-0.04170.21320.0170.224524.0235.93415.955
41.85750.6636-0.33272.46382.0942.30070.014-0.2764-0.05860.3611-0.106-0.028-0.01040.54460.04260.2149-0.0275-0.02740.27950.02020.234125.89430.65116.837
52.8380.543-1.11444.4597-3.42023.27210.1307-0.3607-0.53320.1414-0.357-0.47210.41591.0110.25640.1803-0.0109-0.07160.30760.0630.475123.58420.0614.646
60.23011.3384-1.27537.6755-5.60148.14970.0047-0.0349-0.3631-0.1336-0.08870.09660.198-0.07140.06550.12390.0243-0.05330.1911-0.01390.327716.07122.0710.68
73.05260.1630.39097.7543-4.35494.58560.1386-0.104-0.3217-0.0074-0.23760.19730.0329-0.04490.00050.11590.0019-0.02810.1534-0.00520.205812.50225.91716.874
89.7276.6428-3.09224.8159-2.92036.79920.04540.16090.2296-0.11440.05830.2882-0.6291-0.4662-0.11980.22160.0486-0.0110.1955-0.01480.207411.2634.22219.676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:10 )A2 - 10
2X-RAY DIFFRACTION2( CHAIN A AND RESID 11:40 )A11 - 40
3X-RAY DIFFRACTION3( CHAIN A AND RESID 41:50 )A41 - 50
4X-RAY DIFFRACTION4( CHAIN A AND RESID 51:69 )A51 - 69
5X-RAY DIFFRACTION5( CHAIN A AND RESID 70:83 )A70 - 83
6X-RAY DIFFRACTION6( CHAIN A AND RESID 84:102 )A84 - 102
7X-RAY DIFFRACTION7( CHAIN A AND RESID 103:127 )A103 - 127
8X-RAY DIFFRACTION8( CHAIN A AND RESID 128:137 )A128 - 137

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