[English] 日本語
Yorodumi
- PDB-2aco: Xray structure of Blc dimer in complex with vaccenic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aco
TitleXray structure of Blc dimer in complex with vaccenic acid
ComponentsOuter membrane lipoprotein blc
KeywordsLIPID TRANSPORT / MEMBRANE PROTEIN / lipocalin / fatty acid / E.coli
Function / homology
Function and homology information


cell outer membrane / lipid binding / DNA damage response
Similarity search - Function
Lipocalin, bacterial / : / Lipocalin-like domain / Lipocalin, ApoD type / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Lipocalin, bacterial / : / Lipocalin-like domain / Lipocalin, ApoD type / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
VACCENIC ACID / Outer membrane lipoprotein Blc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCampanacci, V. / Bishop, R.E. / Reese, L. / Blangy, S. / Tegoni, M. / Cambillau, C.
CitationJournal: Febs Lett. / Year: 2006
Title: The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids.
Authors: Campanacci, V. / Bishop, R.E. / Blangy, S. / Tegoni, M. / Cambillau, C.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane lipoprotein blc
B: Outer membrane lipoprotein blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8553
Polymers39,5722
Non-polymers2821
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.901, 81.337, 89.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Outer membrane lipoprotein blc


Mass: 19786.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Tuner pLysS / References: UniProt: P0A901
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID / Vaccenic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate 800-900 mM, sodium borate 50 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→59.76 Å / Num. all: 37259 / Num. obs: 37259 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.089 / Rsym value: 0.137
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.3 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QWD

1qwd


Resolution: 1.8→59.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.334 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21027 2314 5.8 %RANDOM
Rwork0.17093 ---
all0.17325 37259 --
obs0.17325 37259 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.52 Å20 Å2
3----0.08 Å2
Refine analyzeLuzzati coordinate error free: 0.112 Å
Refinement stepCycle: LAST / Resolution: 1.8→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 20 449 3153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212775
X-RAY DIFFRACTIONr_bond_other_d0.0020.022471
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.943752
X-RAY DIFFRACTIONr_angle_other_deg0.79335721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645331
X-RAY DIFFRACTIONr_chiral_restr0.0860.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023107
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02641
X-RAY DIFFRACTIONr_nbd_refined0.2310.2494
X-RAY DIFFRACTIONr_nbd_other0.2580.22973
X-RAY DIFFRACTIONr_nbtor_other0.0820.21650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.243
X-RAY DIFFRACTIONr_mcbond_it0.6791.51652
X-RAY DIFFRACTIONr_mcangle_it1.322650
X-RAY DIFFRACTIONr_scbond_it2.22131123
X-RAY DIFFRACTIONr_scangle_it3.6894.51102
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 143
Rwork0.236 2641

+
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://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