[English] 日本語
Yorodumi
- PDB-3wp9: Crystal structure of antifreeze protein from an Antarctic sea ice... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wp9
TitleCrystal structure of antifreeze protein from an Antarctic sea ice bacterium Colwellia sp.
ComponentsIce-binding protein
KeywordsANTIFREEZE PROTEIN / Right-handed Beta-helix
Function / homologyIce-binding protein / Ice-binding-like / extracellular region / Ice-binding protein
Function and homology information
Biological speciesColwellia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHanada, Y. / Nishimiya, Y. / Miura, A. / Tsuda, S. / Kondo, H.
CitationJournal: Febs J. / Year: 2014
Title: Hyperactive antifreeze protein from an Antarctic sea ice bacterium Colwellia sp. has a compound ice-binding site without repetitive sequences.
Authors: Hanada, Y. / Nishimiya, Y. / Miura, A. / Tsuda, S. / Kondo, H.
History
DepositionJan 10, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ice-binding protein


Theoretical massNumber of molelcules
Total (without water)23,5001
Polymers23,5001
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.250, 106.950, 44.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-352-

HOH

31A-374-

HOH

41A-414-

HOH

51A-494-

HOH

-
Components

#1: Protein Ice-binding protein / antifreeze protein


Mass: 23500.225 Da / Num. of mol.: 1 / Fragment: UNP residues 28-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia (bacteria) / Strain: SLW05 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5XB26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M sodium acetate, 30% polypolyethylene glycol 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→37.17 Å / Num. all: 28529 / Num. obs: 28529 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VN3

3vn3


Resolution: 1.6→37.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.147 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1442 5.1 %RANDOM
Rwork0.19819 ---
obs0.20045 27057 99.64 %-
all-27057 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.057 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 205 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021664
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9612279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34126.2361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.517153
X-RAY DIFFRACTIONr_chiral_restr0.1520.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211243
X-RAY DIFFRACTIONr_mcbond_it2.2412.071895
X-RAY DIFFRACTIONr_mcangle_it2.9373.1031117
X-RAY DIFFRACTIONr_scbond_it3.7982.413768
X-RAY DIFFRACTIONr_long_range_B_refined6.95719.8022655
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 92 -
Rwork0.282 1977 -
obs--99.95 %

+
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://pdbjlvh1.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