[English] 日本語
Yorodumi
- PDB-1kyc: CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kyc
TitleCRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE STABLIZED BY IONIC INTERACTIONS
ComponentsSIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
KeywordsDE NOVO PROTEIN / COILED COIL / DE NOVO DESIGN / ALPHA-HELIX / TRIMER
Function / homologySUCCINIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBurkhard, P. / Ivaninskii, S. / Lustig, A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Improving coiled-coil stability by optimizing ionic interactions.
Authors: Burkhard, P. / Ivaninskii, S. / Lustig, A.
#1: Journal: Protein Sci. / Year: 2000
Title: Design of a Minimal Protein Oligomerization Domain by a Structural Approach
Authors: Burkhard, P. / Meier, M. / Lustig, A.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / struct_conn ...pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
A: SUCCINIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3684
Polymers2,0571
Non-polymers3103
Water41423
1
A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
hetero molecules

A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
hetero molecules

A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,10312
Polymers6,1723
Non-polymers9319
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)33.386, 33.386, 65.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

-
Components

#1: Protein/peptide SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2


Mass: 2057.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized. / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.71 Å3/Da / Density % sol: 28.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.600 mlsatammonium sulfate1reservoir
20.300 mlwater1reservoir
31 MHEPES1reservoirpH7.5
460.0 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 2574 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.54 / Net I/σ(I): 20
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7 / Rsym value: 0.131 / % possible all: 72.1
Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 30 Å / % possible obs: 96.9 % / Num. measured all: 47109 / Rmerge(I) obs: 0.54

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQJ

1hqj


Resolution: 1.45→30 Å / Num. parameters: 1680 / Num. restraintsaints: 2133 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.217 -5 %
Rwork0.166 --
obs-2574 -
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1384 / Occupancy sum non hydrogen: 1815
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms138 0 17 23 178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.4
Refinement
*PLUS
Rfactor Rfree: 0.217 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.4

+
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