[English] 日本語
Yorodumi
- PDB-6w2v: Junction 23, DHR14-DHR18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w2v
TitleJunction 23, DHR14-DHR18
ComponentsJunction 23 DHR14-DHR18
KeywordsBIOSYNTHETIC PROTEIN / helical bundle / designed helical repeat / computational design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.399 Å
AuthorsBick, M.J. / Brunette, T.J. / Baker, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Modular repeat protein sculpting using rigid helical junctions.
Authors: Brunette, T.J. / Bick, M.J. / Hansen, J.M. / Chow, C.M. / Kollman, J.M. / Baker, D.
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Junction 23 DHR14-DHR18
B: Junction 23 DHR14-DHR18


Theoretical massNumber of molelcules
Total (without water)51,4302
Polymers51,4302
Non-polymers00
Water181
1
A: Junction 23 DHR14-DHR18


Theoretical massNumber of molelcules
Total (without water)25,7151
Polymers25,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Junction 23 DHR14-DHR18


Theoretical massNumber of molelcules
Total (without water)25,7151
Polymers25,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.046, 41.084, 94.046
Angle α, β, γ (deg.)90.000, 104.860, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Junction 23 DHR14-DHR18


Mass: 25715.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystals were grown in Qiagen MPD condition A9 (0.2 M Ammonium chloride, 40% MPD) and required no additional cryopreservation

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 17261 / % possible obs: 94.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 69.21 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Χ2: 0.902 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.40.5126330.8380.2450.5710.62672.4
2.44-2.494.60.4456770.9210.2080.4930.71975.2
2.49-2.5350.4397640.950.2020.4850.67183.9
2.53-2.595.30.4398050.9150.1980.4840.67886.3
2.59-2.645.40.4148070.9250.1860.4560.65892.7
2.64-2.75.40.3738740.9420.1680.4110.7594.7
2.7-2.775.30.3138840.9670.1430.3460.78397.1
2.77-2.855.10.2388640.9790.110.2631.00896.3
2.85-2.936.20.239240.9790.0980.251.00599.4
2.93-3.026.30.2128680.9740.0890.231.11299.1
3.02-3.136.30.1799400.9830.0770.1951.0199.5
3.13-3.266.10.1648910.980.0710.1790.95699.6
3.26-3.416.10.1489170.9810.0640.1610.9899.5
3.41-3.585.90.1358900.9660.0610.1490.94798.7
3.58-3.815.70.1169110.990.0520.1270.99697.5
3.81-4.16.40.1069180.9890.0450.1150.9199.4
4.1-4.526.30.0999100.9890.0430.1080.95799.5
4.52-5.1760.0839300.9940.0360.0910.96898.9
5.17-6.5160.0849050.9940.0370.0920.9297.4
6.51-505.70.0699490.9920.0320.0760.93996.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å45.45 Å
Translation3.19 Å45.45 Å

-
Processing

Software
NameVersionClassification
HKL-20002.3.10data scaling
PHASER2.8.0phasing
PHENIXdev-2849refinement
PDB_EXTRACT3.25data extraction
HKL-20002.3.10data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 2.399→45.45 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.01
RfactorNum. reflection% reflection
Rfree0.2713 1642 10.08 %
Rwork0.2437 --
obs0.2465 16290 88.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 345.96 Å2 / Biso mean: 102.6257 Å2 / Biso min: 50.45 Å2
Refinement stepCycle: final / Resolution: 2.399→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 0 1 2763
Biso mean---75.15 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032788
X-RAY DIFFRACTIONf_angle_d0.4293836
X-RAY DIFFRACTIONf_chiral_restr0.031510
X-RAY DIFFRACTIONf_plane_restr0.004506
X-RAY DIFFRACTIONf_dihedral_angle_d13.2991736
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3992-2.46980.3672800.327185663
2.4698-2.54950.36761040.310794870
2.5495-2.64070.34361180.3247105579
2.6407-2.74640.33531440.3141116386
2.7464-2.87130.31251280.3045120488
2.8713-3.02270.36041390.2904128795
3.0227-3.2120.29261600.2829132396
3.212-3.460.3051440.2637135598
3.46-3.8080.28121550.2422132997
3.808-4.35860.23671520.216135599
4.3586-5.48990.25841540.2269137398
5.4899-45.450.25351640.2303140097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0180.1609-0.48371.21140.22.70260.1535-0.12660.38310.16810.00120.13110.08870.2513-0.14990.78170.030.14330.55620.07150.611-3.9654-21.4764-38.1421
21.95520.0272-0.22091.5066-0.10552.7713-0.00740.21050.1228-0.34490.0507-0.0730.1873-0.1625-0.06280.7938-0.00650.15080.60460.08570.5869-17.2191-1.2602-0.3772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 7 through 232)B7 - 232
2X-RAY DIFFRACTION2(chain 'A' and resid 20 through 231)A20 - 231

+
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