[English] 日本語
Yorodumi
- PDB-6syj: Crystal structure of a ProM2 containing triple-helical collagen p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6syj
TitleCrystal structure of a ProM2 containing triple-helical collagen peptide.
ComponentsProM2 containing collagen model peptide.
KeywordsSTRUCTURAL PROTEIN / Collagen model peptide / protein engineering / collagen stability
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.81 Å
AuthorsGebauer, J.M. / Maassen, A. / Schmalz, H.-G. / Baumann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationINST 216/682-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Triple-Helix-Stabilizing Effects in Collagen Model Peptides Containing PPII-Helix-Preorganized Diproline Modules.
Authors: Maassen, A. / Gebauer, J.M. / Theres Abraham, E. / Grimm, I. / Neudorfl, J.M. / Kuhne, R. / Neundorf, I. / Baumann, U. / Schmalz, H.G.
History
DepositionSep 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ProM2 containing collagen model peptide.
B: ProM2 containing collagen model peptide.
C: ProM2 containing collagen model peptide.


Theoretical massNumber of molelcules
Total (without water)8,6773
Polymers8,6773
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, The collagen triple helix was confirmed by CD spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-34 kcal/mol
Surface area4970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.080, 22.850, 53.430
Angle α, β, γ (deg.)90.000, 103.830, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein/peptide ProM2 containing collagen model peptide.


Mass: 2892.248 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.78 Å3/Da / Density % sol: 30.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.1 M (NH4)2HPO4, 0.1 M Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.81→25.26 Å / Num. obs: 57795 / % possible obs: 92.26 % / Redundancy: 6.1 % / CC1/2: 1 / Rmerge(I) obs: 0.03824 / Rpim(I) all: 0.01637 / Rrim(I) all: 0.04171 / Net I/σ(I): 17.74
Reflection shellResolution: 0.81→0.839 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.8166 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 3409 / CC1/2: 0.605 / Rpim(I) all: 0.5215 / Rrim(I) all: 0.9748 / % possible all: 55.12

-
Processing

Software
NameVersionClassification
PHENIX1.17rc5-3630refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AH9

3ah9


Resolution: 0.81→25.26 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1363 1994 3.45 %Random selection (Phenix)
Rwork0.1282 ---
obs-57691 92.26 %-
Displacement parametersBiso mean: 9.55 Å2
Refinement stepCycle: LAST / Resolution: 0.81→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms587 0 0 163 750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0208754
X-RAY DIFFRACTIONf_angle_d1.90661096
X-RAY DIFFRACTIONf_chiral_restr0.074174
X-RAY DIFFRACTIONf_plane_restr0.014180
X-RAY DIFFRACTIONf_dihedral_angle_d16.7764344

+
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