[English] 日本語
Yorodumi
- PDB-1sjv: Three-Dimensional Structure of a Llama VHH Domain Swapping -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sjv
TitleThree-Dimensional Structure of a Llama VHH Domain Swapping
Componentsr9
KeywordsANTIBIOTIC / Camelids antibody / domain swapping / heavy chain antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSpinelli, S. / Desmyter, A. / Frenken, L. / Verrips, T. / Cambillau, C.
CitationJournal: Febs Lett. / Year: 2004
Title: Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure.
Authors: Spinelli, S. / Desmyter, A. / Frenken, L. / Verrips, T. / Tegoni, M. / Cambillau, C.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: r9


Theoretical massNumber of molelcules
Total (without water)12,6401
Polymers12,6401
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: r9

A: r9


Theoretical massNumber of molelcules
Total (without water)25,2802
Polymers25,2802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_554-x+1/4,z+3/4,y-3/41
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area12130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.3, 124.3, 124.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-138-

HOH

-
Components

#1: Antibody r9


Mass: 12640.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: llama VHH single domain antibody / Source: (gene. exp.) Lama glama (llama) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): VWK18 / References: GenBank: 4165546
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 26-28% PEG 600, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.067 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.067 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 12491 / % possible obs: 98.6 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094
Reflection shellResolution: 1.94→2.01 Å / % possible all: 98.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 974 -random
Rwork0.206 ---
all0.207 11053 --
obs0.206 11053 98.34 %-
Refinement stepCycle: LAST / Resolution: 1.94→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 0 59 855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.7

+
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