[English] 日本語
Yorodumi
- PDB-5gs1: Crystal structure of homo-specific diabody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gs1
TitleCrystal structure of homo-specific diabody
Components
  • diabody
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / diabody / antibody fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Lee, H. / Lee, J.O.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningNRF-2014R1A2A1A10050436 Korea, Republic Of
Ministry of Health & WelfareHI15C1886 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.
Authors: Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O.
History
DepositionAug 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: light chain
B: heavy chain
C: diabody
D: diabody
E: diabody
F: diabody
G: diabody
H: diabody
I: diabody
J: diabody
K: diabody
L: diabody
M: light chain
N: heavy chain
O: light chain
P: heavy chain
Q: light chain
R: heavy chain


Theoretical massNumber of molelcules
Total (without water)348,24418
Polymers348,24418
Non-polymers00
Water32,3191794
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.123, 128.807, 259.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody
light chain


Mass: 11654.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody
heavy chain


Mass: 13232.579 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody
diabody


Mass: 24869.445 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1794 / 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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium citrate pH 4.6, 0.2 M Ammonium sulfate, 18% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 248167 / % possible obs: 96.6 % / Redundancy: 5.1 % / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.07 Å

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V7N

2v7n


Resolution: 2→20.046 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 35.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 1991 81 %
Rwork0.2669 --
obs0.267 246850 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→20.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24026 0 0 1794 25820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224650
X-RAY DIFFRACTIONf_angle_d0.61733546
X-RAY DIFFRACTIONf_dihedral_angle_d12.06114250
X-RAY DIFFRACTIONf_chiral_restr0.0443605
X-RAY DIFFRACTIONf_plane_restr0.0044317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.36871340.347816420X-RAY DIFFRACTION91
2.05-2.10530.34911400.340217266X-RAY DIFFRACTION96
2.1053-2.16720.33721410.320917326X-RAY DIFFRACTION96
2.1672-2.23710.34451420.310217445X-RAY DIFFRACTION96
2.2371-2.31690.36041400.306217227X-RAY DIFFRACTION95
2.3169-2.40950.34181410.299917404X-RAY DIFFRACTION96
2.4095-2.5190.321420.289317426X-RAY DIFFRACTION96
2.519-2.65150.2751420.282717483X-RAY DIFFRACTION96
2.6515-2.81720.31861430.273517528X-RAY DIFFRACTION96
2.8172-3.03410.27771430.262117574X-RAY DIFFRACTION97
3.0341-3.33820.28541440.252917849X-RAY DIFFRACTION98
3.3382-3.81830.24291480.229418056X-RAY DIFFRACTION98
3.8183-4.79970.21341460.207417867X-RAY DIFFRACTION97
4.7997-20.04710.25091450.236817988X-RAY DIFFRACTION95

+
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