[English] 日本語
Yorodumi
- PDB-5mhg: Crystal structure of anti-T4 Fab fragment with tetraiodoBPA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mhg
TitleCrystal structure of anti-T4 Fab fragment with tetraiodoBPA
Components(Fab-Fragment) x 2
KeywordsIMMUNE SYSTEM / Fab-fragment / Ig fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TETRAIODOBISPHENOLA
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsParkkinen, T. / Rouvinen, J.
CitationJournal: To Be Published
Title: Crystal structures of anti-T4 Fab fragment
Authors: Parkkinen, T. / Rouvinen, J.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab-Fragment
H: Fab-Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5194
Polymers48,6912
Non-polymers8282
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-38 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.767, 56.992, 61.993
Angle α, β, γ (deg.)90.00, 98.39, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody Fab-Fragment


Mass: 23323.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab-Fragment


Mass: 25367.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-4IB / TETRAIODOBISPHENOLA


Mass: 731.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12I4O2
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium sulfate, 25 % PEG 3350, 0.1 M 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→20.09 Å / Num. obs: 11247 / % possible obs: 98.8 % / Redundancy: 5 % / Net I/σ(I): 6.7
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.21 / CC1/2: 0.53 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MHE

5mhe


Resolution: 2.801→20.09 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.84
RfactorNum. reflection% reflection
Rfree0.291 563 5.01 %
Rwork0.2211 --
obs0.2245 11240 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→20.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 26 0 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013409
X-RAY DIFFRACTIONf_angle_d0.3534647
X-RAY DIFFRACTIONf_dihedral_angle_d8.9842039
X-RAY DIFFRACTIONf_chiral_restr0.037517
X-RAY DIFFRACTIONf_plane_restr0.003585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-3.08180.41821360.32532586X-RAY DIFFRACTION97
3.0818-3.52570.36121410.27472661X-RAY DIFFRACTION100
3.5257-4.43410.29951420.20252701X-RAY DIFFRACTION100
4.4341-20.09070.221440.18282729X-RAY DIFFRACTION100

+
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