[English] 日本語
Yorodumi
- PDB-3c3h: alpha/beta-Peptide helix bundles: A GCN4-pLI analogue with an (al... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c3h
Titlealpha/beta-Peptide helix bundles: A GCN4-pLI analogue with an (alpha-alpha-beta) backbone and cyclic beta residues
Componentsalpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28
KeywordsDE NOVO PROTEIN / helix bundle / foldamer / alpha/beta-peptide / UNKNOWN FUNCTION
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHorne, W.S. / Price, J.L. / Gellman, S.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Interplay among side chain sequence, backbone composition, and residue rigidification in polypeptide folding and assembly.
Authors: Horne, W.S. / Price, J.L. / Gellman, S.H.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Jul 10, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28


Theoretical massNumber of molelcules
Total (without water)4,0251
Polymers4,0251
Non-polymers00
Water23413
1
A: alpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28

A: alpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28

A: alpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28

A: alpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28


Theoretical massNumber of molelcules
Total (without water)16,1004
Polymers16,1004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area5580 Å2
ΔGint-52 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.507, 35.507, 45.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-34-

HOH

-
Components

#1: Protein/peptide alpha/beta-peptide based on the GCN4-pLI side chain sequence, with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19, 22, and 28


Mass: 4024.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.8 Å3/Da / Density % sol: 31.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.7 M diammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Nov 13, 2007 / Details: confocal mirrors
RadiationMonochromator: gobel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35.5 Å / Num. all: 1711 / Num. obs: 1690 / % possible obs: 98.8 % / Redundancy: 5.6 % / Rsym value: 0.098 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.309 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.842 / SU B: 8.658 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27771 73 4.3 %RANDOM
Rwork0.23251 ---
obs0.23468 1606 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.926 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2--1.4 Å20 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms264 0 0 13 277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021271
X-RAY DIFFRACTIONr_bond_other_d0.0020.02202
X-RAY DIFFRACTIONr_angle_refined_deg2.2192.252367
X-RAY DIFFRACTIONr_angle_other_deg1.3583509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.59511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg51.2726.6676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7441538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.247
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.011225
X-RAY DIFFRACTIONr_gen_planes_other00.0139
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.5174
X-RAY DIFFRACTIONr_mcbond_other0.1351.571
X-RAY DIFFRACTIONr_mcangle_it1.2112276
X-RAY DIFFRACTIONr_scbond_it2.219397
X-RAY DIFFRACTIONr_scangle_it3.6914.591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 1 -
Rwork0.278 102 -
obs--88.79 %

+
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