[English] 日本語
Yorodumi
- PDB-6x6q: Peptide-bound structure of Marinomonas primoryensis peptide-bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x6q
TitlePeptide-bound structure of Marinomonas primoryensis peptide-binding domain
Components
  • ASP-SER-ASP
  • Antifreeze protein
KeywordsPROTEIN BINDING / peptide-binding domain / protein-binding domain
Function / homology
Function and homology information


Cadherin-like domain / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Cadherin-like domain / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMarinomonas primoryensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsGuo, S. / Davies, P.L.
Funding support1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)
CitationJournal: Cell Rep / Year: 2021
Title: Molecular basis for inhibition of adhesin-mediated bacterial-host interactions through a peptide-binding domain.
Authors: Guo, S. / Zahiri, H. / Stevens, C. / Spaanderman, D.C. / Milroy, L.G. / Ottmann, C. / Brunsveld, L. / Voets, I.K. / Davies, P.L.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 21, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifreeze protein
B: ASP-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,51820
Polymers53,4002
Non-polymers1,11818
Water8,791488
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.165, 60.717, 63.658
Angle α, β, γ (deg.)66.612, 72.536, 68.582
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Antifreeze protein


Mass: 53064.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3
#2: Protein/peptide ASP-SER-ASP


Mass: 335.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 4.6
Details: ~ 0.1 M calcium chloride, ~ 0.1 M sodium acetate (pH 4.6), ~ 30% (w/v) PEG 400

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→57.55 Å / Num. obs: 41893 / % possible obs: 97.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.02 Å2 / Rrim(I) all: 0.366 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1976 / Rrim(I) all: 0.742

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 58kg

58kg


Resolution: 2.17→57.46 Å / SU ML: 0.204 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.2354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2022 1611 4.9 %
Rwork0.1734 31255 -
obs0.1749 32866 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.68 Å2
Refinement stepCycle: LAST / Resolution: 2.17→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 48 488 4280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753935
X-RAY DIFFRACTIONf_angle_d0.91955386
X-RAY DIFFRACTIONf_chiral_restr0.0826629
X-RAY DIFFRACTIONf_plane_restr0.004731
X-RAY DIFFRACTIONf_dihedral_angle_d15.11741363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.22371280.19392562X-RAY DIFFRACTION97.29
2.23-2.30.23251360.19342604X-RAY DIFFRACTION97.03
2.3-2.390.21781260.18732568X-RAY DIFFRACTION97.5
2.39-2.480.23571390.18672582X-RAY DIFFRACTION97.42
2.48-2.590.21841180.17852606X-RAY DIFFRACTION97.95
2.59-2.730.20431300.16992634X-RAY DIFFRACTION98.05
2.73-2.90.21811360.1742596X-RAY DIFFRACTION98.27
2.9-3.130.1891480.17732605X-RAY DIFFRACTION98.43
3.13-3.440.20421530.16352577X-RAY DIFFRACTION98.48
3.44-3.940.20421420.16262632X-RAY DIFFRACTION98.82
3.94-4.960.15891340.15022628X-RAY DIFFRACTION99.14
4.96-57.460.20661210.19272661X-RAY DIFFRACTION99.5

+
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