[English] 日本語
Yorodumi
- PDB-1ucs: Type III Antifreeze Protein RD1 from an Antarctic Eel Pout -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ucs
TitleType III Antifreeze Protein RD1 from an Antarctic Eel Pout
ComponentsAntifreeze peptide RD1
KeywordsANTIFREEZE PROTEIN / Small Beta Barrel / Pretzel Fold
Function / homology
Function and homology information


extracellular region
Similarity search - Function
SAF domain / SAF domain / Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ice-structuring protein RD1
Similarity search - Component
Biological speciesLycodichthys dearborni (Antarctic eel pout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.62 Å
AuthorsKo, T.-P. / Robinson, H. / Gao, Y.-G. / Cheng, C.-H.C. / DeVries, A.L. / Wang, A.H.-J.
CitationJournal: Biophys.J. / Year: 2003
Title: The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation.
Authors: Ko, T.P. / Robinson, H. / Gao, Y.G. / Cheng, C.H. / DeVries, A.L. / Wang, A.H.
History
DepositionApr 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifreeze peptide RD1


Theoretical massNumber of molelcules
Total (without water)6,9111
Polymers6,9111
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.501, 39.502, 44.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Antifreeze peptide RD1 / Type III Antifreeze Protein RD1


Mass: 6911.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lycodichthys dearborni (Antarctic eel pout)
References: UniProt: P35751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.4 Å3/Da / Density % sol: 11.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
24 mMTris1droppH7.5
320 %ammonium sulfate1drop
450 %ammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.6668 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 23, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6668 Å / Relative weight: 1
ReflectionResolution: 0.62→50 Å / Num. all: 127366 / Num. obs: 118502 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.5
Reflection shellResolution: 0.62→0.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.2 / Num. unique all: 10198 / % possible all: 91.8
Reflection
*PLUS
Lowest resolution: 1.2 Å / Num. obs: 108526 / % possible obs: 97 % / Num. measured all: 256420 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 91.8 % / Num. unique obs: 10198 / Num. measured obs: 18801

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A polypeptide model derived from NMR experiments

Resolution: 0.62→22.32 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: anisotropic model was used in refinement and then the converted to isotropic B values
RfactorNum. reflection% reflectionSelection details
Rfree0.155 5902 -random
Rwork0.133 ---
all0.139 127291 --
obs0.137 118101 92.8 %-
Displacement parametersBiso mean: 8.91 Å2
Refinement stepCycle: LAST / Resolution: 0.62→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 240 1260
Refine LS restraintsType: s_bond_d / Dev ideal: 0.012
LS refinement shellResolution: 0.62→0.65 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.291 582 -
Rwork0.265 --
obs-11845 69.4 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1

+
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