[English] 日本語
Yorodumi
- PDB-1pfc: MOLECULAR-REPLACEMENT STRUCTURE OF GUINEA PIG IGG1 P*FC(PRIME) RE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pfc
TitleMOLECULAR-REPLACEMENT STRUCTURE OF GUINEA PIG IGG1 P*FC(PRIME) REFINED AT 3.1 ANGSTROMS RESOLUTION
ComponentsIGG1 PFC' FC
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / Resolution: 3.125 Å
AuthorsBryant, S.H. / Amzel, L.M. / Poljak, R.J. / Phizackerley, R.P.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: Molecular-Replacement Structure of Guinea Pig Igg1 Pfc(Prime) Refined at 3.1 Angstroms Resolution
Authors: Bryant, S.H. / Amzel, L.M. / Phizackerley, R.P. / Poljak, R.J.
#1: Journal: Thesis, Johns Hopkins University / Year: 1981
Title: Crystallographic Refinement of Guinea Pig Iggi Pfc(Prime) Fragment at 3.125 Angstroms
Authors: Bryant, S.H.
#2: Journal: Mol.Immunol. / Year: 1979
Title: Three Dimensional Structure of the P/Fc(Prime) Fragment of Guinea Pig Igg1
Authors: Phizackerley, R.P. / Wishner, B.C. / Bryant, S.H. / Amzel, L.M. / Lopez Decastro, J.A. / Poljak, R.J.
History
DepositionOct 28, 1981Processing site: BNL
Revision 1.0Feb 3, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IGG1 PFC' FC


Theoretical massNumber of molelcules
Total (without water)12,6901
Polymers12,6901
Non-polymers00
Water00
1
A: IGG1 PFC' FC

A: IGG1 PFC' FC


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)60.570, 60.570, 136.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein IGG1 PFC' FC


Mass: 12690.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal grow
*PLUS
Method: unknown

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

RefinementResolution: 3.125→5 Å / Rfactor Rwork: 0.303
Refinement stepCycle: LAST / Resolution: 3.125→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 0 0 878
Refinement
*PLUS
Rfactor obs: 0.303
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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