[English] 日本語
Yorodumi
- PDB-7qwd: CC-Type2-(Ug)4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qwd
TitleCC-Type2-(Ug)4
ComponentsCC-Type2-(Ug)4
KeywordsDE NOVO PROTEIN / aib / coiled coil / pentamer / 2-Aminoisobutyric acid
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsMartin, F.J.O. / Zieleniewski, F. / Dawson, W.M. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)340764 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB R00661X 1 United Kingdom
CitationJournal: To Be Published
Title: CC-Type2-(Ug)4
Authors: Martin, F.J.O. / Zieleniewski, F. / Dawson, W.M. / Woolfson, D.N.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Type2-(Ug)4
B: CC-Type2-(Ug)4
C: CC-Type2-(Ug)4
D: CC-Type2-(Ug)4
E: CC-Type2-(Ug)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7496
Polymers16,6545
Non-polymers951
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-91 kcal/mol
Surface area7910 Å2
Unit cell
Length a, b, c (Å)34.108, 48.994, 89.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 30
2010B1 - 30
1020A1 - 30
2020C1 - 30
1030A1 - 30
2030D1 - 30
1040A1 - 30
2040E1 - 30
1050B1 - 30
2050C1 - 30
1060B1 - 30
2060D1 - 30
1070B1 - 30
2070E1 - 30
1080C1 - 30
2080D1 - 30
1090C1 - 30
2090E1 - 30
10100D1 - 30
20100E1 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

#1: Protein/peptide
CC-Type2-(Ug)4


Mass: 3330.839 Da / Num. of mol.: 5 / Mutation: W19BrPhe / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.5 mM peptide, 50 mM SPG, 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: I24 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.35→43 Å / Num. obs: 32660 / % possible obs: 97.52 % / Redundancy: 76.4 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.4586 / Rpim(I) all: 0.04872 / Rrim(I) all: 0.4612 / Net I/σ(I): 11.11
Reflection shellResolution: 1.354→1.403 Å / Redundancy: 47.5 % / Mean I/σ(I) obs: 0.25 / Num. unique obs: 2788 / CC1/2: 0.357 / CC star: 0.725 / Rpim(I) all: 1.529 / Rrim(I) all: 10.61 / % possible all: 85.21

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.98 / SU ML: 0.079 / SU R Cruickshank DPI: 0.0726 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1614 5 %RANDOM
Rwork0.2144 ---
obs0.2161 30975 97.55 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.85 Å2 / Biso mean: 23.86 Å2 / Biso min: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å2-0 Å2
2---1.91 Å20 Å2
3---3.01 Å2
Refinement stepCycle: final / Resolution: 1.35→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 5 66 1194
Biso mean--49.38 31.11 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131134
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171282
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6341529
X-RAY DIFFRACTIONr_angle_other_deg7.9121.5882919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.175141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23228.38731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12315234
X-RAY DIFFRACTIONr_chiral_restr0.0770.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02182
X-RAY DIFFRACTIONr_rigid_bond_restr3.11732416
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8000.14
12B8000.14
21A7860.13
22C7860.13
31A8150.12
32D8150.12
41A8310.11
42E8310.11
51B8020.14
52C8020.14
61B8250.13
62D8250.13
71B8250.12
72E8250.12
81C7980.12
82D7980.12
91C7990.12
92E7990.12
101D8340.11
102E8340.11
LS refinement shellResolution: 1.354→1.389 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 109 -
Rwork0.379 1838 -
all-1947 -
obs--80.96 %
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)
18.6451-2.8995-6.01853.69772.06058.4657-0.33010.4007-0.2607-0.16640.0510.14960.2025-0.44550.27910.0517-0.02380.00720.0463-0.00810.01315.9987-0.37452.9002
24.46361.1633-4.71271.8082-1.735710.7787-0.0928-0.26350.2060.16130.0437-0.2810.01310.21370.04910.05380.0364-0.03890.034-0.03350.089928.43125.32564.9437
39.46112.5364-8.49832.344-2.510612.2493-0.1859-0.0342-0.20980.0294-0.0605-0.38410.30360.12790.24640.03020.0177-0.00990.01860.01220.069429.3271-2.264559.6819
42.645-0.4477-4.50392.17380.439813.442-0.0368-0.05820.24820.09390.089-0.0476-0.2363-0.1795-0.05220.02290.0251-0.01940.0298-0.01820.048920.99847.359359.6213
57.0299-0.4482-6.20652.8070.02979.9107-0.17460.0732-0.3305-0.07930.0178-0.20650.4486-0.15650.15680.03080.00020.00740.01630.0020.041521.9582-4.912356.4122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B0 - 30
3X-RAY DIFFRACTION3C0 - 30
4X-RAY DIFFRACTION4D1 - 30
5X-RAY DIFFRACTION5E1 - 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://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