[English] 日本語
Yorodumi
- PDB-7rmx: Structure of De Novo designed tunable symmetric protein pockets -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rmx
TitleStructure of De Novo designed tunable symmetric protein pockets
ComponentsTunable symmetric protein, D_3_212
KeywordsDE NOVO PROTEIN / De novo DESIGN / tunable / symmetric protein / pockets
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBera, A.K. / Hicks, D.R. / Kang, A. / Sankaran, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo design of protein homodimers containing tunable symmetric protein pockets.
Authors: Hicks, D.R. / Kennedy, M.A. / Thompson, K.A. / DeWitt, M. / Coventry, B. / Kang, A. / Bera, A.K. / Brunette, T.J. / Sankaran, B. / Stoddard, B. / Baker, D.
History
DepositionJul 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tunable symmetric protein, D_3_212


Theoretical massNumber of molelcules
Total (without water)26,5641
Polymers26,5641
Non-polymers00
Water1,72996
1
A: Tunable symmetric protein, D_3_212

A: Tunable symmetric protein, D_3_212


Theoretical massNumber of molelcules
Total (without water)53,1282
Polymers53,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.091, 97.212, 36.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein Tunable symmetric protein, D_3_212


Mass: 26563.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20000, glycerol, sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, MES/imidazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 25328 / % possible obs: 99.04 % / Redundancy: 7.7 % / Biso Wilson estimate: 25.92 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.59
Reflection shellResolution: 1.64→1.7 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2417 / CC1/2: 0.821

-
Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: De novo Designed Model

Resolution: 1.65→48.61 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 1309 5.17 %
Rwork0.1861 24006 -
obs0.1876 25315 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 0 96 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091919
X-RAY DIFFRACTIONf_angle_d0.96592586
X-RAY DIFFRACTIONf_chiral_restr0.0512307
X-RAY DIFFRACTIONf_plane_restr0.0063331
X-RAY DIFFRACTIONf_dihedral_angle_d20.68611228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.3231300.29252565X-RAY DIFFRACTION96.73
1.71-1.790.31041510.26432598X-RAY DIFFRACTION98.92
1.79-1.890.29271260.23532640X-RAY DIFFRACTION99.18
1.89-20.24211500.21432646X-RAY DIFFRACTION99.29
2-2.160.19331500.18612656X-RAY DIFFRACTION99.43
2.16-2.380.21791450.17712670X-RAY DIFFRACTION99.75
2.38-2.720.23321440.17832681X-RAY DIFFRACTION99.86
2.72-3.430.20621610.18752738X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 1.20700788503 Å / Origin y: -11.7881850341 Å / Origin z: 6.09969566996 Å
111213212223313233
T0.213181494222 Å20.0155785162321 Å2-0.0220312759095 Å2-0.204316473239 Å2-0.0189409564753 Å2--0.153395961828 Å2
L1.71839776833 °20.455069963608 °20.0857030677986 °2-1.41101117217 °2-0.073791460588 °2--0.279279051399 °2
S0.0114627355855 Å °0.0344007257472 Å °-0.0349822306762 Å °0.046597506906 Å °-0.0456228499592 Å °0.0778549581528 Å °-0.016592212191 Å °-0.0336834816772 Å °0.0237538462162 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://pdbjlc1.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