[English] 日本語
Yorodumi
- PDB-7rkc: Computationally designed tunable C2 symmetric tandem repeat homod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rkc
TitleComputationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633
ComponentsD_3_633
KeywordsDE NOVO PROTEIN / de novo / torroid / derroid / tandem repeat / homodimer / computationally designed / C2 symmetric
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsKennedy, M.A. / Stoddard, B.L. / Hicks, D.R. / Bera, A.K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1762114 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139752 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)U19AG065156 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 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D_3_633
B: D_3_633
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5517
Polymers54,2562
Non-polymers2955
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.445, 54.682, 86.987
Angle α, β, γ (deg.)90.000, 95.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 and (name N or name...
21(chain B and (resid 4 or (resid 5 through 6...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and ((resid 4 and (name N or name...AA49
12ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
13ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
14ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
15ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
16ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
17ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
21ASPASPASPASP(chain B and (resid 4 or (resid 5 through 6...BB49
22GLUGLULEULEU(chain B and (resid 4 or (resid 5 through 6...BB5 - 610 - 11
23GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231
24GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231
25GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231
26GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231

-
Components

#1: Protein D_3_633


Mass: 27127.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Zinc acetate, 0.1 M Na acetate pH 4.5, 10% PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 21194 / % possible obs: 96.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Χ2: 1.06 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.394.11.02911100.6580.5811.1840.607100
2.39-2.434.20.80710530.7160.4530.9280.621100
2.43-2.484.20.66510930.8050.3720.7640.641100
2.48-2.534.20.5810840.8120.3270.6680.663100
2.53-2.594.20.50310970.8710.2820.5780.702100
2.59-2.654.20.44710870.8830.2520.5140.742100
2.65-2.714.10.410760.9050.2250.4611.10199.8
2.71-2.794.20.30310950.9360.1710.3490.778100
2.79-2.874.20.23110950.960.1290.2650.874100
2.87-2.964.20.19310750.9640.1080.2211.027100
2.96-3.074.10.16511110.9730.0940.191.206100
3.07-3.194.10.14310740.9790.0810.1651.351100
3.19-3.334.10.13411050.9810.0750.1541.32599.9
3.33-3.5130.1569740.9590.10.1862.21589.9
3.51-3.732.90.219990.8830.1480.2592.67790.4
3.73-4.022.30.1296020.9620.0940.1611.95355.1
4.02-4.4240.07210860.9910.0420.0841.054100
4.42-5.064.10.05411260.9960.0310.0621.235100
5.06-6.374.10.04611190.9970.0250.0521.161100
6.37-5040.03511330.9970.020.041.19298

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.32 Å48.05 Å
Translation2.32 Å48.05 Å

-
Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: computationally generated

Resolution: 2.35→48.05 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3119 1996 9.44 %
Rwork0.2693 19138 -
obs0.2734 21134 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.62 Å2 / Biso mean: 73.1269 Å2 / Biso min: 32.19 Å2
Refinement stepCycle: final / Resolution: 2.35→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 20 5 2968
Biso mean--76.22 67.25 -
Num. residues----436
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1262X-RAY DIFFRACTION4.51TORSIONAL
12B1262X-RAY DIFFRACTION4.51TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.380.35741220.32371171129382
2.38-2.450.3511480.301714191567100
2.45-2.520.36171480.30314151563100
2.52-2.60.33931500.293614501600100
2.6-2.690.33861470.295514021549100
2.69-2.80.32931480.286714131561100
2.8-2.930.32291500.277514351585100
2.93-3.080.39511490.296214321581100
3.08-3.280.36311480.297214241572100
3.28-3.530.35261380.31511321145992
3.53-3.880.36171150.32551101121676
3.88-4.440.26581270.24821224135186
4.45-5.60.28751520.234314521604100
5.6-48.050.27061540.23691479163398
Refinement TLS params.Method: refined / Origin x: 10.0951 Å / Origin y: -1.0503 Å / Origin z: 23.0787 Å
111213212223313233
T0.3669 Å20.0865 Å2-0.0507 Å2-0.3383 Å2-0.0013 Å2--0.3862 Å2
L2.8229 °20.6539 °2-1.2057 °2-1.2261 °2-0.3332 °2--3.3097 °2
S-0.136 Å °0.0598 Å °0.023 Å °-0.1154 Å °0.019 Å °-0.0057 Å °-0.0578 Å °0.0656 Å °0.1088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 228
2X-RAY DIFFRACTION1allB2 - 226
3X-RAY DIFFRACTION1allD1 - 5
4X-RAY DIFFRACTION1allS1 - 7

+
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