[English] 日本語
Yorodumi
- PDB-5b3n: The crystal structure of anti-H4K20me1_scFv, 15F11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b3n
TitleThe crystal structure of anti-H4K20me1_scFv, 15F11
Componentsanti-H4K20me1_scFv
KeywordsIMMUNE SYSTEM / Histone modification / scFv / intrabody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsKujirai, T. / Horikoshi, N. / Kurumizaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
the Ministry of Education, Culture, Sports, Science and Technology25116002 Japan
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation
Authors: Sato, Y. / Kujirai, T. / Arai, R. / Asakawa, H. / Ohtsuki, C. / Horikoshi, N. / Yamagata, K. / Ueda, J. / Nagase, T. / Haraguchi, T. / Hiraoka, Y. / Kimura, A. / Kurumizaka, H. / Kimura, H.
History
DepositionMar 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 2.0Jul 5, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / diffrn_source / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.src_method / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.2Nov 8, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti-H4K20me1_scFv


Theoretical massNumber of molelcules
Total (without water)27,2461
Polymers27,2461
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10580 Å2
Unit cell
Length a, b, c (Å)130.825, 130.825, 130.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

-
Components

#1: Antibody anti-H4K20me1_scFv


Mass: 27246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Sodium acetate, poly-gamma-glutamic acid polymer, and PEG2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2015
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 29161 / % possible obs: 99.9 % / Redundancy: 28 % / Biso Wilson estimate: 20.15 Å2 / Rmerge(I) obs: 0.099 / Net I/av σ(I): 24.714 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.94-2.0111.80.403199.4
2.01-2.0913.50.3771100
2.09-2.18150.3381100
2.18-2.315.90.298199.9
2.3-2.4420.40.2681100
2.44-2.6323.30.222199.9
2.63-2.928.80.165199.9
2.9-3.3240.80.12199.9
3.32-4.1851.20.0821100
4.18-5054.90.073199.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000706cdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
PHASER2.5.1phasing
HKL-2000706cdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHW

2ghw


Resolution: 1.94→43.608 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.58
RfactorNum. reflection% reflection
Rfree0.2439 1463 5.06 %
Rwork0.2031 --
obs0.2051 28897 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.11 Å2 / Biso mean: 22.4597 Å2 / Biso min: 10.2 Å2
Refinement stepCycle: final / Resolution: 1.94→43.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 135 1926
Biso mean---25.82 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081834
X-RAY DIFFRACTIONf_angle_d1.0852486
X-RAY DIFFRACTIONf_chiral_restr0.042270
X-RAY DIFFRACTIONf_plane_restr0.005320
X-RAY DIFFRACTIONf_dihedral_angle_d14.25658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9401-2.00950.32151450.30626782823
2.0095-2.08990.34851330.28926852818
2.0899-2.1850.30681460.259727062852
2.185-2.30020.27311390.242726812820
2.3002-2.44430.26491560.225927032859
2.4443-2.6330.25651540.225427142868
2.633-2.8980.24851460.206627312877
2.898-3.31720.23991500.201227482898
3.3172-4.17880.2121430.15828042947
4.1788-43.61930.18471510.155329843135

+
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