[English] 日本語
Yorodumi
- PDB-7dc5: Crystal structure of fungal antifreeze protein with intermediate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dc5
TitleCrystal structure of fungal antifreeze protein with intermediate activity
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / right-handed beta-helix / beta-solenoid / ice-binding protein / thermal hysteresis protein / ice-structuring protein
Function / homologyIce-binding protein / Ice-binding-like / Antifreeze protein
Function and homology information
Biological speciesTyphula ishikariensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsKhan, N.M.M.U. / Arai, T. / Tsuda, S. / Kondo, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)KAKENHI JP20570118 Japan
CitationJournal: Sci Rep / Year: 2021
Title: Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity.
Authors: Khan, N.M.U. / Arai, T. / Tsuda, S. / Kondo, H.
History
DepositionOct 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 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: Antifreeze protein
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6328
Polymers44,0552
Non-polymers5766
Water13,439746
1
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2203
Polymers22,0281
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-19 kcal/mol
Surface area8590 Å2
MethodPISA
2
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4125
Polymers22,0281
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.122, 62.991, 101.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Antifreeze protein


Mass: 22027.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Typhula ishikariensis (fungus) / Gene: K1-C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76CE7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH6.5, 30% (w/v) PEG MME 5000, 0.2M ammonium sulfate
PH range: 6.5

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.54→49.8 Å / Num. obs: 54671 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.038 / Rrim(I) all: 0.136 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.54-1.5713.11.16726200.9410.3361.21599.1
8.43-49.89.70.0593800.9970.020.06294.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å49.75 Å
Translation2.5 Å49.75 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5H

5b5h


Resolution: 1.54→49.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.988 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1001 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 2734 5 %RANDOM
Rwork0.1946 ---
obs0.1963 51912 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.33 Å2 / Biso mean: 9.79 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 1.54→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 30 746 3878
Biso mean--27.55 18.58 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133213
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173007
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.6384414
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5596974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09724.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.81615464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.467155
X-RAY DIFFRACTIONr_chiral_restr0.0770.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 187 -
Rwork0.457 3742 -
all-3929 -
obs--98.82 %

+
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