[English] 日本語
Yorodumi
- PDB-6ugc: C3 symmetric peptide design number 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ugc
TitleC3 symmetric peptide design number 3
ComponentsC3-3 cyclic peptide design
KeywordsDE NOVO PROTEIN / cyclic peptide / 3-fold symmetric / racemic mixture
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.9 Å
Model detailsS2 symmetric cyclic peptide
AuthorsMulligan, V.K. / Kang, C.S. / Antselovich, I. / Sawaya, M.R. / Yeates, T.O. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Computational design of mixed chirality peptide macrocycles with internal symmetry.
Authors: Mulligan, V.K. / Kang, C.S. / Sawaya, M.R. / Rettie, S. / Li, X. / Antselovich, I. / Craven, T.W. / Watkins, A.M. / Labonte, J.W. / DiMaio, F. / Yeates, T.O. / Baker, D.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C3-3 cyclic peptide design
B: C3-3 cyclic peptide design
C: C3-3 cyclic peptide design
D: C3-3 cyclic peptide design
E: C3-3 cyclic peptide design
F: C3-3 cyclic peptide design
G: C3-3 cyclic peptide design
H: C3-3 cyclic peptide design
I: C3-3 cyclic peptide design
J: C3-3 cyclic peptide design
K: C3-3 cyclic peptide design
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,17939
Polymers10,99911
Non-polymers1,18028
Water1,910106
1
A: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • Evidence: cyclic peptide
  • 1.18 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1815
Polymers1,0001
Non-polymers1814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 1.18 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1815
Polymers1,0001
Non-polymers1814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 1.02 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0232
Polymers1,0001
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 1.16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1584
Polymers1,0001
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 1.23 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2277
Polymers1,0001
Non-polymers2276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 1.16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1584
Polymers1,0001
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: C3-3 cyclic peptide design
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0232
Polymers1,0001
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 1.16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1584
Polymers1,0001
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: C3-3 cyclic peptide design
hetero molecules

I: C3-3 cyclic peptide design
hetero molecules

I: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 3.07 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)3,0696
Polymers3,0003
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
10
J: C3-3 cyclic peptide design
hetero molecules

J: C3-3 cyclic peptide design
hetero molecules

J: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 3.07 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)3,0696
Polymers3,0003
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
11
K: C3-3 cyclic peptide design
hetero molecules

K: C3-3 cyclic peptide design
hetero molecules

K: C3-3 cyclic peptide design
hetero molecules


  • defined by author
  • 3.07 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)3,0696
Polymers3,0003
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Unit cell
Length a, b, c (Å)51.030, 51.030, 36.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number159
Space group name H-MP31c
Components on special symmetry positions
IDModelComponents
11I-101-

NA

21J-101-

NA

31K-101-

NA

41I-203-

HOH

51J-201-

HOH

61K-203-

HOH

-
Components

#1: Protein/peptide
C3-3 cyclic peptide design


Mass: 999.886 Da / Num. of mol.: 11 / Source method: obtained synthetically / Details: de novo design / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFor chains I,J,K the asymmetric unit contains one third of the molecule. The whole molecule is ...For chains I,J,K the asymmetric unit contains one third of the molecule. The whole molecule is generated by crystallographic symmetry operators.
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.53 Å3/Da / Density % sol: 19.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Cadmium chloride, 0.1 M Sodium acetate pH 4.6, 30% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 17, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.9→25.51 Å / Num. obs: 30646 / % possible obs: 78.7 % / Redundancy: 2.242 % / Biso Wilson estimate: 7.496 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.112 / Χ2: 0.949 / Net I/σ(I): 5.85 / Num. measured all: 68716
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.9-0.922.3880.4642.164533285718980.8540.57266.4
0.92-0.952.4530.3462.724713282419210.8990.42568
0.95-0.982.430.2633.284693272419310.9420.32370.9
0.98-1.012.3850.2313.64592267119250.9520.28672.1
1.01-1.042.2440.2193.824198256118710.9610.27273.1
1.04-1.082.3530.1964.294563247819390.9580.24578.2
1.08-1.122.3060.1415.364443240819270.9720.17880
1.12-1.162.2560.1295.544268231018920.9760.16381.9
1.16-1.212.2020.1215.823953219617950.9790.15581.7
1.21-1.272.1190.1046.223551212716760.9860.13478.8
1.27-1.342.1810.0926.813841200617610.9850.11887.8
1.34-1.422.1550.0867.153566191116550.9840.11286.6
1.42-1.522.1010.0737.523303178315720.9880.09888.2
1.52-1.642.0860.0758.093020168214480.9870.186.1
1.64-1.82.0750.0668.792531151912200.9870.08980.3
1.8-2.012.0840.0619.62655138712740.9840.08391.9
2.01-2.322.0850.0669.792333121511190.9840.08892.1
2.32-2.852.1290.07110.15187610338810.9840.09485.3
2.85-4.032.1610.06110.213037926030.9930.0876.1
4.03-25.512.3110.0789.477814403380.9870.10476.8

-
Processing

Software
NameVersionClassification
XDS20190315data reduction
XSCALE20190315data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
SHELXDSHELXT actually, but was not available on this menuphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→25.51 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.374 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1429 3065 10 %RANDOM
Rwork0.118 ---
obs0.1205 27581 78.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 53.44 Å2 / Biso mean: 7.195 Å2 / Biso min: 1.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å2-0 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 0.9→25.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 31 110 762
Biso mean--7.45 14.1 -
Num. residues----82
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013722
X-RAY DIFFRACTIONr_bond_other_d0.0020.016444
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.7161005
X-RAY DIFFRACTIONr_angle_other_deg0.8231.6891130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.572588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1753064
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9351563
X-RAY DIFFRACTIONr_chiral_restr0.1410.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02889
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0271
X-RAY DIFFRACTIONr_rigid_bond_restr3.62531166
LS refinement shellResolution: 0.9→0.923 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 190 -
Rwork0.241 1706 -
all-1896 -
obs--66.41 %

+
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