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- PDB-2w9y: The structure of the lipid binding protein Ce-FAR-7 from Caenorha... -

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Basic information

Entry
Database: PDB / ID: 2w9y
TitleThe structure of the lipid binding protein Ce-FAR-7 from Caenorhabditis elegans
ComponentsFATTY ACID/RETINOL BINDING PROTEIN PROTEIN 7, ISOFORM A, CONFIRMED BY TRANSCRIPT EVIDENCE
KeywordsLIPID TRANSPORT / FATTY ACID AND RETINOID BINDING
Function / homology
Function and homology information


oleic acid binding / extracellular region / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1100 / Nematode fatty acid retinoid binding / Nematode fatty acid retinoid binding protein (Gp-FAR-1) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Fatty Acid/Retinol binding protein
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJordanova, R. / Groves, M.R. / Tucker, P.A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Fatty Acid and Retinoid Binding Proteins Have Distinct Binding Pockets for the Two Types of Cargo
Authors: Jordanova, R. / Groves, M.R. / Kostova, E.B. / Woltersdorf, C. / Liebau, E. / Tucker, P.A.
History
DepositionJan 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Apr 9, 2025Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID/RETINOL BINDING PROTEIN PROTEIN 7, ISOFORM A, CONFIRMED BY TRANSCRIPT EVIDENCE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7353
Polymers15,5431
Non-polymers1922
Water3,261181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.850, 41.600, 101.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FATTY ACID/RETINOL BINDING PROTEIN PROTEIN 7, ISOFORM A, CONFIRMED BY TRANSCRIPT EVIDENCE / CE-FAR-7


Mass: 15542.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES GA (N-TERMINUS) ARE FROM THE HIS TAG, C9 IS CSX (CYSTEINE SULFENIC ACID)
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9TZ51
#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.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGA IN THE N-TERMINUS ARE FROM THE HIS TAG, THESE RESIDUES ARE NOT IN Q9TZ51

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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: 2.3 Å3/Da / Density % sol: 46 %
Description: THIS IS THE NATIVE DATASET, USED FOR THE REFINEMENT. THE STRUCTURE WAS SOLVED WITH SESAD FROM THE ADDITIONAL DATASET, GIVEN BELOW.
Crystal growpH: 7.5 / Details: 20MM TRIS PH 7.8-8.5, 2.1-2.9M AMMONIUM SULFATE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-210.8726
SYNCHROTRONESRF ID2920.97926
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDJun 15, 2008PT COATED MIRRORS IN KB GEOMETRY
ADSC CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI (111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.979261
ReflectionResolution: 1.79→50 Å / Num. obs: 13757 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.13
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.19 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→50.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.542 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 42, 43, 44 AND 45 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 690 5 %RANDOM
Rwork0.171 ---
obs0.174 13156 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 10 181 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.67621513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7255145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54125.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61515211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.735154
X-RAY DIFFRACTIONr_chiral_restr0.1240.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6951.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.60821143
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0993414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.154.5366
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 54
Rwork0.226 933
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)
10.4756-0.0085-0.21540.33150.24780.3235-0.00480.02950.02920.00460.0070.01280.00330.0124-0.00220.00830.0017-0.00160.01180.0030.0605-0.65122.10217.301
23.93270.58850.07631.43040.89473.5432-0.12370.32190.3098-0.19290.09610.0132-0.30240.09840.02760.0384-0.0196-0.01130.03040.01890.05897.82219.0910.087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 27
2X-RAY DIFFRACTION1A57 - 138
3X-RAY DIFFRACTION2A28 - 41
4X-RAY DIFFRACTION2A46 - 56

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