[English] 日本語
Yorodumi
- PDB-7dgw: De novo designed protein H4A2S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dgw
TitleDe novo designed protein H4A2S
Componentsde novo designed protein H4A2S
KeywordsDE NOVO PROTEIN / Designed protein
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsXu, Y. / Liao, S. / Chen, Q. / Liu, H.
CitationJournal: Nature / Year: 2022
Title: A backbone-centred energy function of neural networks for protein design.
Authors: Huang, B. / Xu, Y. / Hu, X. / Liu, Y. / Liao, S. / Zhang, J. / Huang, C. / Hong, J. / Chen, Q. / Liu, H.
History
DepositionNov 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description / _struct.title
Revision 1.3Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: de novo designed protein H4A2S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5882
Polymers11,3491
Non-polymers2381
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area5580 Å2
Unit cell
Length a, b, c (Å)46.526, 53.801, 30.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein de novo designed protein H4A2S


Mass: 11349.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.68 Å3/Da / Density % sol: 26.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 20% PEG 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.35→35.192 Å / Num. obs: 17343 / % possible obs: 99.5 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 29
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 0.248 / Num. unique obs: 1641 / CC1/2: 0.986

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→35.192 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 1734 10 %
Rwork0.1909 15609 -
obs0.1944 17343 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.77 Å2 / Biso mean: 22.6246 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 1.35→35.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 0 84 792
Biso mean---33.84 -
Num. residues----94
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.38930.34291370.2644122294
1.3893-1.43410.28361390.2281126999
1.4341-1.48540.26251420.2121280100
1.4854-1.54490.22031420.1852128399
1.5449-1.61520.21631430.19621278100
1.6152-1.70030.21891430.196129299
1.7003-1.80690.25431450.19411297100
1.8069-1.94640.2481430.20651292100
1.9464-2.14220.24481470.18921323100
2.1422-2.45210.20561470.18041314100
2.4521-3.08910.22411500.19071350100
3.0891-35.1920.21011560.18191409100
Refinement TLS params.Method: refined / Origin x: 29.219 Å / Origin y: 13.59 Å / Origin z: 22.6902 Å
111213212223313233
T0.134 Å20.0085 Å20.0062 Å2-0.1221 Å20.0001 Å2--0.1403 Å2
L0.9631 °20.3551 °2-0.0171 °2-0.3624 °2-0.1747 °2--1.3949 °2
S-0.0703 Å °-0.0486 Å °-0.0052 Å °-0.0041 Å °0.004 Å °-0.0198 Å °0.0297 Å °-0.036 Å °-0.0011 Å °
Refinement TLS groupSelection details: all

+
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