[English] 日本語
Yorodumi
- PDB-7qdi: Structure of octameric left-handed 310-helix bundle: D-310HD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qdi
TitleStructure of octameric left-handed 310-helix bundle: D-310HD
ComponentsD-310HD
KeywordsDE NOVO PROTEIN / octamer / 310-helix / LL core
Function / homologyBORIC ACID / DI(HYDROXYETHYL)ETHER / Chem-PG6 / TRIETHYLENE GLYCOL / polypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å
AuthorsKumar, P. / Paterson, N.G. / Woolfson, D.N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 United Kingdom
CitationJournal: Nature / Year: 2022
Title: De novo design of discrete, stable 3 10 -helix peptide assemblies.
Authors: Kumar, P. / Paterson, N.G. / Clayden, J. / Woolfson, D.N.
History
DepositionNov 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 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 1.2Jul 6, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-310HD
B: D-310HD
C: D-310HD
D: D-310HD
E: D-310HD
F: D-310HD
G: D-310HD
H: D-310HD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,05940
Polymers27,0488
Non-polymers3,01132
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.238, 44.976, 194.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 30
2010B2 - 30
1020A1 - 29
2020C1 - 29
1030A2 - 29
2030D2 - 29
1040A1 - 29
2040E1 - 29
1050A2 - 29
2050F2 - 29
1060A1 - 29
2060G1 - 29
1070A2 - 29
2070H2 - 29
1080B2 - 29
2080C2 - 29
1090B2 - 29
2090D2 - 29
10100B2 - 29
20100E2 - 29
10110B2 - 29
20110F2 - 29
10120B2 - 29
20120G2 - 29
10130B2 - 29
20130H2 - 29
10140C2 - 29
20140D2 - 29
10150C1 - 30
20150E1 - 30
10160C2 - 29
20160F2 - 29
10170C1 - 30
20170G1 - 30
10180C2 - 29
20180H2 - 29
10190D2 - 29
20190E2 - 29
10200D2 - 30
20200F2 - 30
10210D2 - 29
20210G2 - 29
10220D2 - 30
20220H2 - 30
10230E2 - 29
20230F2 - 29
10240E1 - 30
20240G1 - 30
10250E2 - 29
20250H2 - 29
10260F2 - 29
20260G2 - 29
10270F2 - 30
20270H2 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27

-
Components

-
Polypeptide(D) , 1 types, 8 molecules ABCDEFGH

#1: Polypeptide(D)
D-310HD


Mass: 3380.969 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: A 310-helix comprising mostly D-amino acids / Source: (synth.) synthetic construct (others)

-
Non-polymers , 9 types, 100 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#8: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), 25% w/v PEG 1500 at pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9204 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
ReflectionResolution: 2.34→29.59 Å / Num. obs: 12818 / % possible obs: 97.13 % / Redundancy: 10.9 % / Biso Wilson estimate: 42.54 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1138 / Rpim(I) all: 0.03584 / Rrim(I) all: 0.1196 / Net I/σ(I): 11.97
Reflection shellResolution: 2.34→2.425 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.062 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 1056 / CC1/2: 0.824 / CC star: 0.951 / Rpim(I) all: 0.3265 / % possible all: 83.68

-
Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→29.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 15.647 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 594 4.7 %RANDOM
Rwork0.1885 ---
obs0.191 12063 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.58 Å2 / Biso mean: 49.263 Å2 / Biso min: 26.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.21 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 2.34→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 194 68 2070
Biso mean--73.33 62.55 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0141970
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162355
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.7312699
X-RAY DIFFRACTIONr_angle_other_deg1.1491.6215278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515230
X-RAY DIFFRACTIONr_chiral_restr0.1190.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021786
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02254
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A7010.14
12B7010.14
21A6950.12
22C6950.12
31A6760.14
32D6760.14
41A7050.11
42E7050.11
51A6660.14
52F6660.14
61A7050.1
62G7050.1
71A6660.17
72H6660.17
81B6730.14
82C6730.14
91B7110.09
92D7110.09
101B6770.15
102E6770.15
111B7040.12
112F7040.12
121B6810.14
122G6810.14
131B6960.15
132H6960.15
141C6730.14
142D6730.14
151C7280.1
152E7280.1
161C6670.14
162F6670.14
171C7300.13
172G7300.13
181C6640.16
182H6640.16
191D6750.13
192E6750.13
201D7320.11
202F7320.11
211D6780.12
212G6780.12
221D7170.16
222H7170.16
231E6750.13
232F6750.13
241E7310.12
242G7310.12
251E6750.17
252H6750.17
261F6750.14
262G6750.14
271F7130.15
272H7130.15
LS refinement shellResolution: 2.342→2.402 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 35 -
Rwork0.282 700 -
all-735 -
obs--78.11 %
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)
11.2685-0.87771.99592.3968-4.11949.8005-0.02350.04590.0301-0.17090.0105-0.01490.0836-0.21760.0130.03380.00420.01220.0354-0.02180.0535-7.68232.6738126.8147
21.352-0.10262.70571.2983-1.258310.64650.08270.11810.0091-0.1021-0.07520.04450.2556-0.0333-0.00750.01760.00920.01540.0437-0.01360.066-1.88623.1377124.5217
31.54060.66552.88881.80172.704310.70830.06140.16840.01610.0385-0.031-0.0150.3750.0481-0.03040.0206-0.00340.00830.03370.01150.0495.21213.8207127.1794
41.20970.06390.11272.18593.099210.3226-0.17890.10930.0542-0.1148-0.02710.09740.06250.25090.2060.0403-0.0038-0.01070.03680.03590.07555.10249.7506124.4779
52.064-1.3817-2.45912.48463.14077.0703-0.019-0.0174-0.0332-0.10760.0039-0.0323-0.12430.27010.01510.0109-0.0056-0.00440.03520.03050.07284.819317.5605127.1308
62.4759-0.5602-3.99631.87391.040210.31510.09060.13870.0559-0.101-0.0534-0.0597-0.2831-0.003-0.03720.03250.0022-0.03880.0216-0.00020.0838-1.02217.1649124.3065
72.28751.1957-3.54461.8967-2.97438.68360.11640.12340.0597-0.02760.03720.0575-0.23550.0024-0.15360.02550.0033-0.01420.0256-0.0180.0611-8.266416.4892126.4795
81.3830.6158-0.85042.0861-1.88698.2699-0.02270.11860.0428-0.09660.0632-0.009-0.0607-0.2284-0.04040.008-0.00060.00510.0287-0.03210.0898-7.676911.0366123.8372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2B2 - 31
3X-RAY DIFFRACTION3C1 - 30
4X-RAY DIFFRACTION4D2 - 30
5X-RAY DIFFRACTION5E1 - 30
6X-RAY DIFFRACTION6F2 - 30
7X-RAY DIFFRACTION7G1 - 30
8X-RAY DIFFRACTION8H2 - 30

+
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://pdbjlvh1.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