[English] 日本語
Yorodumi
- PDB-1kd8: X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kd8
TitleX-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L
Components
  • GCN4 ACID BASE HETERODIMER ACID-d12Ia16V
  • GCN4 ACID BASE HETERODIMER BASE-d12La16L
KeywordsDE NOVO PROTEIN / coiled coil heterodimer
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKeating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.
Authors: Keating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GCN4 ACID BASE HETERODIMER ACID-d12Ia16V
B: GCN4 ACID BASE HETERODIMER BASE-d12La16L
C: GCN4 ACID BASE HETERODIMER ACID-d12Ia16V
D: GCN4 ACID BASE HETERODIMER BASE-d12La16L
E: GCN4 ACID BASE HETERODIMER BASE-d12La16L
F: GCN4 ACID BASE HETERODIMER ACID-d12Ia16V


Theoretical massNumber of molelcules
Total (without water)24,8996
Polymers24,8996
Non-polymers00
Water5,188288
1
A: GCN4 ACID BASE HETERODIMER ACID-d12Ia16V
B: GCN4 ACID BASE HETERODIMER BASE-d12La16L


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-22 kcal/mol
Surface area5150 Å2
MethodPISA
2
C: GCN4 ACID BASE HETERODIMER ACID-d12Ia16V
D: GCN4 ACID BASE HETERODIMER BASE-d12La16L


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-23 kcal/mol
Surface area5300 Å2
MethodPISA
3
E: GCN4 ACID BASE HETERODIMER BASE-d12La16L
F: GCN4 ACID BASE HETERODIMER ACID-d12Ia16V


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-23 kcal/mol
Surface area5280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.044, 86.044, 78.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-42-

HOH

DetailsThe assembly is a dimer. There are three copies of the dimer intact in the asymmetric unit.

-
Components

#1: Protein/peptide GCN4 ACID BASE HETERODIMER ACID-d12Ia16V / GABH AIV


Mass: 4142.462 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#2: Protein/peptide GCN4 ACID BASE HETERODIMER BASE-d12La16L / GABH BLL


Mass: 4157.150 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.91 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 4000, Na Hepes, 2-propanol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
218-20 %PEG40001reservoir
30.1 Msodium HEPES1reservoirpH7.7
410 %2-propanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. all: 25471 / Num. obs: 25471 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.413 / % possible all: 99
Reflection
*PLUS
Rmerge(I) obs: 0.06

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: calculated structure

Resolution: 1.9→28.97 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2395 10.2 %random
Rwork0.232 ---
all-23529 --
obs-23529 98.9 %-
Solvent computationSolvent model: flat model / Bsol: 62.63 Å2 / ksol: 0.386808 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 0 288 1992
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d13.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 381 9.9 %
Rwork0.263 3469 -
obs--99.3 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.232 / Rfactor Rfree: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg0.99
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.328 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.263

+
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://pdbjlvh1.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