[English] 日本語
Yorodumi
- PDB-6x9p: 2-deoxyribose-bound structure of Marinomonas primoryensis PA14 ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x9p
Title2-deoxyribose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / 2-deoxyribose-MpPA14 complex / PA14 domain / carbohydrate-binding protein
Function / homology
Function and homology information


Cadherin-like domain / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold
Similarity search - Domain/homology
2-deoxy-beta-D-ribopyranose / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsGuo, S. / Davies, P.L.
Funding support1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)
Citation
Journal: Mbio / Year: 2021
Title: Structural Basis of Ligand Selectivity by a Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation.
Authors: Guo, S. / Vance, T.D.R. / Zahiri, H. / Eves, R. / Stevens, C. / Hehemann, J.H. / Vidal-Melgosa, S. / Davies, P.L.
#1: Journal: To Be Published
Title: Molecular basis for a bacterial adhesins sugar-binding module
Authors: Guo, S.
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,89011
Polymers20,3081
Non-polymers58310
Water5,441302
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)45.220, 50.530, 79.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Antifreeze protein


Mass: 20307.580 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3
#2: Chemical ChemComp-UZJ / 2-deoxy-beta-D-ribopyranose / 2-deoxy-beta-D-erythro-pentopyranose


Mass: 134.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 0.2 M calcium chloride, 0.1 M HEPES (pH 7), 20% (v/v) polyethylene glycol 3350 and 30% (w/v) 2-deoxy-ribose

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 0.96→39.74 Å / Num. obs: 106580 / % possible obs: 95.76 % / Redundancy: 11.1 % / Biso Wilson estimate: 8.69 Å2 / Rpim(I) all: 0.018 / Net I/σ(I): 17.8
Reflection shellResolution: 0.96→1 Å / Num. unique obs: 7177 / Rpim(I) all: 1.468

-
Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j6y

5j6y


Resolution: 1→39.73 Å / SU ML: 0.095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.8735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1416 4911 5 %
Rwork0.129 93291 -
obs0.1296 98202 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.87 Å2
Refinement stepCycle: LAST / Resolution: 1→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 30 302 1707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831492
X-RAY DIFFRACTIONf_angle_d1.22152039
X-RAY DIFFRACTIONf_chiral_restr0.1323225
X-RAY DIFFRACTIONf_plane_restr0.008270
X-RAY DIFFRACTIONf_dihedral_angle_d17.2631508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.35611450.35052757X-RAY DIFFRACTION88.58
1.01-1.020.32551520.30932898X-RAY DIFFRACTION94.08
1.02-1.040.24091600.26343035X-RAY DIFFRACTION97.74
1.04-1.050.22491620.20513076X-RAY DIFFRACTION99.75
1.05-1.060.20321610.17673065X-RAY DIFFRACTION99.45
1.06-1.080.2061650.1653128X-RAY DIFFRACTION99.55
1.08-1.090.14131610.15523059X-RAY DIFFRACTION99.41
1.09-1.110.15041630.14513090X-RAY DIFFRACTION99.72
1.11-1.130.14431640.13063120X-RAY DIFFRACTION99.94
1.13-1.140.12651620.11393080X-RAY DIFFRACTION99.94
1.14-1.160.11821640.10513104X-RAY DIFFRACTION100
1.16-1.190.12181640.09893109X-RAY DIFFRACTION100
1.19-1.210.11131630.0973110X-RAY DIFFRACTION100
1.21-1.230.11581650.09563129X-RAY DIFFRACTION100
1.23-1.260.11631630.09853103X-RAY DIFFRACTION99.97
1.26-1.290.10931640.09493122X-RAY DIFFRACTION100
1.29-1.320.12581630.09783093X-RAY DIFFRACTION99.97
1.32-1.360.1181640.09943107X-RAY DIFFRACTION100
1.36-1.40.11811640.09533111X-RAY DIFFRACTION100
1.4-1.440.11921660.09883153X-RAY DIFFRACTION99.97
1.44-1.490.10981640.09733135X-RAY DIFFRACTION100
1.49-1.550.11141650.09773117X-RAY DIFFRACTION100
1.55-1.620.10781660.13153X-RAY DIFFRACTION100
1.62-1.710.14181640.10713134X-RAY DIFFRACTION100
1.71-1.820.121680.11463174X-RAY DIFFRACTION100
1.82-1.960.15091650.12473148X-RAY DIFFRACTION100
1.96-2.150.13211680.11863181X-RAY DIFFRACTION99.94
2.15-2.470.12551680.13173198X-RAY DIFFRACTION100
2.47-3.110.16961690.1473218X-RAY DIFFRACTION99.91
3.11-39.730.15811790.15723384X-RAY DIFFRACTION99.92

+
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