[English] 日本語
Yorodumi
- PDB-5cwc: Crystal structure of de novo designed helical repeat protein DHR5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cwc
TitleCrystal structure of de novo designed helical repeat protein DHR5
ComponentsDesigned helical repeat protein
KeywordsDE NOVO PROTEIN / helical repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.25 Å
AuthorsBhabha, G. / Ekiert, D.C.
CitationJournal: Nature / Year: 2015
Title: Exploring the repeat protein universe through computational protein design.
Authors: Brunette, T.J. / Parmeggiani, F. / Huang, P.S. / Bhabha, G. / Ekiert, D.C. / Tsutakawa, S.E. / Hura, G.L. / Tainer, J.A. / Baker, D.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Designed helical repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8222
Polymers23,7601
Non-polymers621
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.320, 51.140, 72.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Designed helical repeat protein


Mass: 23759.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% (w/v) PEG 6000, 1 M Lithium chloride, 0.1 M Bis-Tris, pH 7.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.111
SYNCHROTRONALS 8.3.121.714
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: DOUBLE FLAT CRYSTAL, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1111
21.7141
ReflectionNumber: 556066 / Rmerge(I) obs: 0.078 / Χ2: 1.04 / D res high: 1.85 Å / Num. obs: 28741 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
1.851.9196610.502
1.91.95203310.393
1.952.01200810.3
2.012.07200310.224
2.072.14191210.178
2.142.21184910.135
2.212.29179410.111
2.292.39172610.098
2.392.49162410.092
2.492.62158810.084
2.622.76147010.079
2.762.93141810.075
2.933.13134710.07
3.133.38123610.068
3.383.7113110.063
3.74.14102510.06
4.144.7892110.06
4.785.8576510.064
5.858.2759410.054
ReflectionResolution: 1.25→50 Å / Num. obs: 47733 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 14.92 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.054 / Χ2: 0.972 / Net I/σ(I): 18.21 / Num. measured all: 334858
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.25-1.285.70.651.5271.1716444361528771.67579.6
1.28-1.320.81.2191.6322954353533461.31894.7
1.32-1.360.8581.0022.0323851345033021.07895.7
1.36-1.40.8730.8712.3323205334332100.93796
1.4-1.440.9340.6553.0822513323031150.70696.4
1.44-1.490.9780.3795.0321927313930360.40896.7
1.49-1.550.9860.286.7721369304629600.30197.2
1.55-1.610.9910.2348.0420398289728180.25297.3
1.61-1.690.9910.1939.7719780281127420.20897.5
1.69-1.770.9950.14312.8819092270526550.15598.2
1.77-1.860.9960.10916.6218101255225170.11798.6
1.86-1.980.9980.08520.9217285245524140.09198.3
1.98-2.110.9990.05928.6116107227022510.06499.2
2.11-2.280.9990.04237.9915081215721340.04698.9
2.28-2.50.9990.03446.3413718198419670.03799.1
2.5-2.80.9990.0351.7612126180517810.03398.7
2.8-3.2310.02559.0310956159215800.02799.2
3.23-3.950.9990.02267.139355138013640.02498.8
3.95-5.590.9990.02169.547072108310710.02398.9
5.590.9990.02262.4935246585930.02490.1

-
Phasing

Phasing
Method
SAD
molecular replacement

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHELXphasing
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.25→41.858 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 2380 5 %RANDOM
Rwork0.1412 45259 --
obs0.1424 47639 95.94 %-
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.97 Å2 / Biso mean: 27.4934 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.25→41.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 10 209 1752
Biso mean--34.3 39.33 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071962
X-RAY DIFFRACTIONf_angle_d0.9692649
X-RAY DIFFRACTIONf_chiral_restr0.05272
X-RAY DIFFRACTIONf_plane_restr0.004377
X-RAY DIFFRACTIONf_dihedral_angle_d13.606842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.27550.33511120.33472130224278
1.2755-1.30330.33231220.30292509263193
1.3033-1.33360.27711610.27082576273795
1.3336-1.3670.25571280.2392652278096
1.367-1.40390.24751380.21732619275796
1.4039-1.44520.26091340.18922657279196
1.4452-1.49190.18121420.15252633277596
1.4919-1.54520.19421400.13172677281797
1.5452-1.60710.15491520.11762654280697
1.6071-1.68020.15111350.11212717285297
1.6802-1.76880.15751430.10352701284498
1.7688-1.87960.15841410.10712733287499
1.8796-2.02470.13391440.1052741288599
2.0247-2.22850.15321450.09952767291299
2.2285-2.55090.11891460.10472790293699
2.5509-3.21370.15451500.13492810296099
3.2137-41.88170.16811470.16582893304097

+
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