[English] 日本語
Yorodumi
- PDB-9lhs: Crystal structure of an ice-binding protein from Candidatus Cryos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lhs
TitleCrystal structure of an ice-binding protein from Candidatus Cryosericum odellii
ComponentsDUF3494 domain-containing protein
KeywordsPROTEIN BINDING / Ice binding protein / Antifreeze protein / DUF3494 / Ice affinity / Candidatus Cryosericum odellii SMC5
Function / homologyIce-binding protein / Ice-binding-like / : / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / DUF3494 domain-containing protein
Function and homology information
Biological speciesCandidatus Cryosericum odellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsHoang, T. / Do, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentKIMST 20200610 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Ice affinity purification system for recombinant proteins using a DUF3494 ice-binding protein.
Authors: Hoang, T. / Nguyen, D.L. / Kim, B. / Choi, W. / Cho, S.M. / Kim, H.W. / Han, S.J. / Kim, K. / Lee, J.H. / Do, H.
History
DepositionJan 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF3494 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,8801
Polymers22,8801
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.810, 66.810, 142.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21A-513-

HOH

-
Components

#1: Protein DUF3494 domain-containing protein / Ice binding domain


Mass: 22879.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Ice Binding Domain (DUF3494) region was truncated from CoIBP3 (WP_119120131.1)
Source: (gene. exp.) Candidatus Cryosericum odellii (bacteria)
Gene: SMC5_06950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A398DEW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.5 M sodium formate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→29.259 Å / Num. obs: 29297 / % possible obs: 100 % / Redundancy: 25.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.2
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 1774

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→29.259 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.006 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2094 1430 4.881 %
Rwork0.1772 27867 -
all0.179 --
obs-29297 99.945 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.933 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å20 Å20 Å2
2---0.006 Å20 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 215 1785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151527
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.632191
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5643503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68824.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.25315224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.353152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
X-RAY DIFFRACTIONr_nbd_refined0.1970.2256
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21335
X-RAY DIFFRACTIONr_nbtor_refined0.1560.2791
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.25
X-RAY DIFFRACTIONr_nbd_other0.1360.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.24
X-RAY DIFFRACTIONr_mcbond_it1.9812.6899
X-RAY DIFFRACTIONr_mcbond_other1.9782.596898
X-RAY DIFFRACTIONr_mcangle_it2.4733.8861122
X-RAY DIFFRACTIONr_mcangle_other2.4743.891123
X-RAY DIFFRACTIONr_scbond_it2.9282.82698
X-RAY DIFFRACTIONr_scbond_other2.9232.821698
X-RAY DIFFRACTIONr_scangle_it4.0194.1251069
X-RAY DIFFRACTIONr_scangle_other4.0194.1291070
X-RAY DIFFRACTIONr_lrange_it4.8732.7771697
X-RAY DIFFRACTIONr_lrange_other4.74332.0781652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.8780.251080.222023X-RAY DIFFRACTION99.9062
1.878-1.9290.2351030.1881954X-RAY DIFFRACTION100
1.929-1.9850.21100.1721907X-RAY DIFFRACTION100
1.985-2.0460.223870.1771862X-RAY DIFFRACTION100
2.046-2.1130.2071140.1741777X-RAY DIFFRACTION99.9472
2.113-2.1870.221940.1751754X-RAY DIFFRACTION100
2.187-2.2690.282750.1761704X-RAY DIFFRACTION100
2.269-2.3620.216780.1731648X-RAY DIFFRACTION100
2.362-2.4670.206710.1791579X-RAY DIFFRACTION100
2.467-2.5870.266790.1891502X-RAY DIFFRACTION100
2.587-2.7260.241730.2011430X-RAY DIFFRACTION100
2.726-2.8920.215770.2081368X-RAY DIFFRACTION100
2.892-3.0910.265640.2161283X-RAY DIFFRACTION100
3.091-3.3380.261550.2061227X-RAY DIFFRACTION100
3.338-3.6550.18540.1711116X-RAY DIFFRACTION100
3.655-4.0850.187550.1471013X-RAY DIFFRACTION100
4.085-4.7130.137490.126914X-RAY DIFFRACTION100
4.713-5.7630.177360.15789X-RAY DIFFRACTION100
5.763-8.1140.233250.179638X-RAY DIFFRACTION100
8.114-29.2590.157230.193379X-RAY DIFFRACTION96.8675

+
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