[English] 日本語
Yorodumi
- PDB-7tmh: Porous framework formed by assembly of a bipyridyl-conjugated hel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tmh
TitlePorous framework formed by assembly of a bipyridyl-conjugated helical peptide
Componentshelical peptide
KeywordsDE NOVO PROTEIN / porous / framework / helix / 310 / alpha / assembly / bipyridine / UIC-1
Function / homologyACETONITRILE / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.8 Å
AuthorsNguyen, A.I.
Funding support1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Assembly of pi-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework.
Authors: Heinz-Kunert, S.L. / Pandya, A. / Dang, V.T. / Tran, P.N. / Ghosh, S. / McElheny, D. / Santarsiero, B.D. / Ren, Z. / Nguyen, A.I.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: helical peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7435
Polymers1,1471
Non-polymers5964
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.608, 13.513, 27.424
Angle α, β, γ (deg.)90.000, 97.094, 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 helical peptide


Mass: 1147.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-I77 / 5'-(hydrazinecarbonyl)[2,2'-bipyridine]-5-carboxamide


Mass: 257.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N5O2
#3: Chemical ChemComp-I6W / ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate


Mass: 256.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O3
#4: Chemical ChemComp-CCN / ACETONITRILE / Acetonitrile


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 295 K / Method: slow cooling / Details: water and acetonitrile

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.688 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688 Å / Relative weight: 1
ReflectionResolution: 0.8→13.5 Å / Num. obs: 19340 / % possible obs: 95.43 % / Redundancy: 6.7 % / Biso Wilson estimate: 4.95 Å2 / Rrim(I) all: 0.05818 / Net I/σ(I): 26.34
Reflection shellResolution: 0.83→0.8597 Å / Num. unique obs: 1826 / Rrim(I) all: 0.1462

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TLS

7tls


Resolution: 0.8→13.5 Å / SU ML: 0.0456 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 13.0185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1272 1946 10.06 %
Rwork0.1153 17394 -
obs0.1165 19340 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 6.85 Å2
Refinement stepCycle: LAST / Resolution: 0.8→13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90 0 25 5 120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119152
X-RAY DIFFRACTIONf_angle_d1.8997208
X-RAY DIFFRACTIONf_chiral_restr0.059614
X-RAY DIFFRACTIONf_plane_restr0.007324
X-RAY DIFFRACTIONf_dihedral_angle_d31.43426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8-0.820.17521260.15931112X-RAY DIFFRACTION87.93
0.82-0.840.14521400.14921230X-RAY DIFFRACTION91.76
0.84-0.870.15681390.14491235X-RAY DIFFRACTION96.56
0.87-0.890.16911370.12921226X-RAY DIFFRACTION92.09
0.89-0.930.14391380.12161257X-RAY DIFFRACTION97.01
0.93-0.960.13181440.10891249X-RAY DIFFRACTION92.74
0.96-1.010.11121350.10831247X-RAY DIFFRACTION96.44
1.01-1.060.10281320.09861189X-RAY DIFFRACTION90.98
1.06-1.130.09521480.09691310X-RAY DIFFRACTION96.24
1.13-1.210.08761380.09241262X-RAY DIFFRACTION98.31
1.21-1.340.1141440.09941297X-RAY DIFFRACTION97.56
1.34-1.530.13041450.10371269X-RAY DIFFRACTION96.13
1.53-1.930.12321370.11561238X-RAY DIFFRACTION93.66
1.93-13.50.1461430.13091273X-RAY DIFFRACTION98.81

+
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