[English] 日本語
Yorodumi
- PDB-2w9y: The structure of the lipid binding protein Ce-FAR-7 from Caenorha... -

+
Open data


ID or keywords:

Loading...

-
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 / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #1100 / Nematode fatty acid retinoid binding / Nematode fatty acid retinoid binding protein (Gp-FAR-1) / oleic acid binding / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / cytoplasm / Fatty Acid/Retinol binding protein
Function and homology information
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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Sequence detailsGA IN THE N-TERMINUS ARE FROM THE HIS TAG, THESE RESIDUES ARE NOT IN Q9TZ51

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more