[English] 日本語
Yorodumi
- PDB-6g65: Crystal structure of a parallel six-helix coiled coil CC-Type2-VV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g65
TitleCrystal structure of a parallel six-helix coiled coil CC-Type2-VV
ComponentsCC-Type2-VV
KeywordsDE NOVO PROTEIN / de novo / coiled coil / alpha-helical bundle / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / AB_INITIO / Resolution: 1.15 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Maintaining and breaking symmetry in homomeric coiled-coil assemblies.
Authors: Rhys, G.G. / Wood, C.W. / Lang, E.J.M. / Mulholland, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Type2-VV
B: CC-Type2-VV
C: CC-Type2-VV
D: CC-Type2-VV
E: CC-Type2-VV
F: CC-Type2-VV
G: CC-Type2-VV
H: CC-Type2-VV
I: CC-Type2-VV
J: CC-Type2-VV
K: CC-Type2-VV
L: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)37,47212
Polymers37,47212
Non-polymers00
Water6,305350
1
A: CC-Type2-VV
B: CC-Type2-VV
C: CC-Type2-VV

A: CC-Type2-VV
B: CC-Type2-VV
C: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10260 Å2
ΔGint-85 kcal/mol
Surface area9380 Å2
MethodPISA
2
D: CC-Type2-VV
E: CC-Type2-VV
F: CC-Type2-VV

D: CC-Type2-VV
E: CC-Type2-VV
F: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10210 Å2
ΔGint-96 kcal/mol
Surface area9320 Å2
MethodPISA
3
G: CC-Type2-VV
H: CC-Type2-VV
I: CC-Type2-VV

G: CC-Type2-VV
H: CC-Type2-VV
I: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9810 Å2
ΔGint-92 kcal/mol
Surface area9460 Å2
MethodPISA
4
J: CC-Type2-VV
K: CC-Type2-VV
L: CC-Type2-VV

J: CC-Type2-VV
K: CC-Type2-VV
L: CC-Type2-VV


Theoretical massNumber of molelcules
Total (without water)18,7366
Polymers18,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10400 Å2
ΔGint-81 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.561, 96.793, 56.400
Angle α, β, γ (deg.)90.000, 124.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-139-

HOH

21B-140-

HOH

31B-141-

HOH

41B-142-

HOH

51E-131-

HOH

61E-132-

HOH

71F-130-

HOH

81F-131-

HOH

91G-134-

HOH

101G-135-

HOH

111G-136-

HOH

121I-135-

HOH

131K-129-

HOH

141L-123-

HOH

-
Components

#1: Protein/peptide
CC-Type2-VV


Mass: 3122.655 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: solid-phase peptide synthesis using the fmoc-based strategy
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 1.98 Å3/Da / Density % sol: 37.85 % / Mosaicity: 0.42 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 5 mM Manganese(II) chloride tetrahydrate, 50 mM Sodium citrate and 1.25 M 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.15→14.28 Å / Num. obs: 99219 / % possible obs: 96.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 7.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 13.7 / Num. measured all: 622875 / Scaling rejects: 336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.15-1.176.30.32849900.9860.1440.35997.9
6.3-14.287.50.0685950.9920.030.07591.5

-
Phasing

PhasingMethod: AB_INITIO

-
Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.25data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
Arcimboldo4.0.0phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.15→13.88 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.07
RfactorNum. reflection% reflection
Rfree0.1896 5029 5.1 %
Rwork0.1761 --
obs0.1767 98638 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.99 Å2 / Biso mean: 13.3263 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 1.15→13.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 0 350 3002
Biso mean---30.18 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072892
X-RAY DIFFRACTIONf_angle_d0.683934
X-RAY DIFFRACTIONf_chiral_restr0.042459
X-RAY DIFFRACTIONf_plane_restr0.004488
X-RAY DIFFRACTIONf_dihedral_angle_d19.2631088
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16310.24651900.20193086327697
1.1631-1.17680.19262010.20363108330996
1.1768-1.19110.21781590.19153097325695
1.1911-1.20620.1971530.18783088324195
1.2062-1.2220.19541590.17543128328796
1.222-1.23880.19181520.17463116326895
1.2388-1.25640.17231240.17283115323995
1.2564-1.27520.14611730.16023040321394
1.2752-1.29510.18121720.153000317292
1.2951-1.31630.17651870.1542970315792
1.3163-1.3390.16681990.15963164336398
1.339-1.36330.16521720.16073152332498
1.3633-1.38950.18351570.16093222337998
1.3895-1.41790.1731560.16243145330197
1.4179-1.44870.16671800.15843160334097
1.4487-1.48230.15791680.14963149331797
1.4823-1.51930.14621620.14373082324495
1.5193-1.56040.15761600.14253085324594
1.5604-1.60620.14661740.1442943311791
1.6062-1.6580.16671600.14163197335798
1.658-1.71710.16551950.15523190338599
1.7171-1.78570.17052170.15533134335198
1.7857-1.86680.17511600.15793210337098
1.8668-1.9650.18441290.17913176330597
1.965-2.08770.18021580.19153132329095
2.0877-2.24830.17461460.16352973311991
2.2483-2.47340.17481520.1643188334098
2.4734-2.82870.23721630.19153275343899
2.8287-3.55390.19861890.1923218340798
3.5539-13.88130.26471620.23953066322892
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)
10.23620.0754-0.02250.0521-0.09370.1836-0.0133-0.02910.03130.4926-0.0211-0.2977-0.00390.0203-0.00180.10770.0109-0.03070.0722-0.00170.06425.77129.41877.1043
20.16460.02430.10050.15360.07920.31350.0265-0.0013-0.01860.0407-0.06030.38320.0381-0.0254-0.10350.0656-0.00210.020.0761-0.00830.09537.916446.787824.9912
30.19030.11530.07560.05540.02990.14240.0175-0.0092-0.01670.268-0.0560.18810.00890.006300.09330.00450.01920.06780.00140.0502-3.032729.12728.6432
40.1854-0.0983-0.10150.04790.04850.1586-0.0060.00630.0018-0.3374-0.05120.25750.0290.0009-00.0950.0029-0.01470.0672-0.00630.0711.189847.530816.1398
50.21-0.03930.03010.0498-0.0820.14250.02380.0047-0.0057-0.0715-0.0456-0.3470.00390.0245-0.00040.06770.0020.01080.065-0.00110.07069.069128.67-1.6755
60.1926-0.1089-0.01590.0613-0.02320.074-0.02490.0018-0.0366-0.3779-0.0254-0.1466-0.00340.0263-0.00010.10360.00430.02650.06940.00330.061320.154347.039314.758
70.23760.14290.01360.1171-0.04940.08640.0044-0.01140.00440.4701-0.0168-0.089-0.00860.0050.00010.10890.0044-0.01350.0671-0.00080.0471.978677.9588.9942
80.14030.02720.06860.06580.10650.18450.05170.0024-0.01050.2569-0.07920.2181-0.0043-0.0145-0.00010.0669-0.00330.02010.06760.00030.07199.8151-0.560529.4746
90.07530.10210.07740.0740.0950.21590.0137-0.0104-0.03030.3339-0.0290.3762-0.0206-0.0095-0.00040.08030.00510.03430.07070.00530.0765-6.692377.82776.3651
100.03040.0222-0.11240.0828-0.1740.25850.0218-0.00690.0060.2792-0.0266-0.57440.00490.0094-0.09490.05960.0023-0.03320.0729-0.0050.12319.151577.72922.7924
110.2557-0.1142-0.00880.15420.00670.01060.04620.0321-0.0023-0.578-0.09710.0547-0.00430.0058-0.00130.12150.0049-0.01150.070.00020.056615.2157-0.71914.1341
120.0928-0.0843-0.1370.07660.15990.30460.06690.0199-0.006-0.1148-0.08850.55990.0019-0.009-0.00210.04540.0006-0.02750.06860.0010.11018.2793-1.173620.4274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 30 )H1 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 30 )A1 - 30
3X-RAY DIFFRACTION3chain 'G' and (resid 1 through 30 )G1 - 30
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 30 )B1 - 30
5X-RAY DIFFRACTION5chain 'I' and (resid 1 through 30 )I1 - 30
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 30 )C1 - 30
7X-RAY DIFFRACTION7chain 'K' and (resid 1 through 30 )K1 - 30
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 30 )D1 - 30
9X-RAY DIFFRACTION9chain 'J' and (resid 1 through 30 )J1 - 30
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 30 )L1 - 30
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 30 )F1 - 30
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 30 )E1 - 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://pdbjlc1.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