[English] 日本語
Yorodumi
- PDB-8vhs: X-ray Structure of a De Novo Designed Self Assembled Peptide Tetr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vhs
TitleX-ray Structure of a De Novo Designed Self Assembled Peptide Tetramer Featuring a Cu(His)4(H2O) Coordination Motif
ComponentsCu-4SCC
KeywordsDE NOVO PROTEIN / De novo design / Peptides / Self-assembly / Copper
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsChakraborty, S. / Mitra, S. / Prakash, D. / Prasad, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Nat Commun / Year: 2025
Title: Controlling outer-sphere solvent reorganization energy to turn on or off the function of artificial metalloenzymes.
Authors: Prakash, D. / Mitra, S. / Sony, S. / Murphy, M. / Andi, B. / Ashley, L. / Prasad, P. / Chakraborty, S.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cu-4SCC
B: Cu-4SCC
C: Cu-4SCC
D: Cu-4SCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1185
Polymers16,0554
Non-polymers641
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-69 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.410, 45.470, 97.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide
Cu-4SCC


Mass: 4013.703 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH8.5, 2 M ammonium sulfate, peptide concentration 45 mg/mL with 1 equivalent Cu2+

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.36→26.52 Å / Num. obs: 54455 / % possible obs: 98.36 % / Redundancy: 1.1 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 10.68
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 1 % / Num. unique obs: 887 / CC1/2: 1 / CC star: 1 / Net I/σ(I) obs: 0.55 / % possible all: 88.94

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R4A

3r4a


Resolution: 1.36→26.52 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2253 1260 4.89 %
Rwork0.1955 --
obs0.1968 25780 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→26.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 1 101 1209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.887
X-RAY DIFFRACTIONf_dihedral_angle_d19.656166
X-RAY DIFFRACTIONf_chiral_restr0.05185
X-RAY DIFFRACTIONf_plane_restr0.004213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.410.26911140.25292427X-RAY DIFFRACTION89
1.41-1.480.24951390.2272642X-RAY DIFFRACTION97
1.48-1.560.22981620.20012696X-RAY DIFFRACTION99
1.56-1.650.23211470.18272711X-RAY DIFFRACTION100
1.65-1.780.2321590.19962710X-RAY DIFFRACTION100
1.78-1.960.24341260.1882764X-RAY DIFFRACTION100
1.96-2.240.20211370.1892783X-RAY DIFFRACTION100
2.24-2.830.23721240.1892823X-RAY DIFFRACTION100
2.83-26.520.21841520.19752965X-RAY DIFFRACTION100

+
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