[English] 日本語
Yorodumi
- PDB-1k8u: CRYSTAL STRUCTURE OF CALCIUM-FREE (OR APO) HUMAN S100A6; CYS3MET ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k8u
TitleCRYSTAL STRUCTURE OF CALCIUM-FREE (OR APO) HUMAN S100A6; CYS3MET MUTANT (SELENOMETHIONINE DERIVATIVE)
ComponentsS100A6
KeywordsSIGNALING PROTEIN / S100A6 / CALCYCLIN / CALCIUM REGULATORY PROTEIN / CALCIUM FREE / APO / CACY
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / calcium-dependent protein binding / positive regulation of fibroblast proliferation / nuclear envelope / collagen-containing extracellular matrix ...monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / calcium-dependent protein binding / positive regulation of fibroblast proliferation / nuclear envelope / collagen-containing extracellular matrix / calcium ion binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsOtterbein, L.R. / Dominguez, R.
CitationJournal: Structure / Year: 2002
Title: Crystal structures of S100A6 in the Ca(2+)-free and Ca(2+)-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution.
Authors: Otterbein, L.R. / Kordowska, J. / Witte-Hoffmann, C. / Wang, C.L. / Dominguez, R.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S100A6


Theoretical massNumber of molelcules
Total (without water)10,3161
Polymers10,3161
Non-polymers00
Water2,108117
1
A: S100A6

A: S100A6


Theoretical massNumber of molelcules
Total (without water)20,6312
Polymers20,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area9140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.259, 48.113, 83.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: x, -y, -z+1

-
Components

#1: Protein S100A6 / / CALCYCLIN / CACY


Mass: 10315.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pLYS / References: UniProt: P06703
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 1500, 30mM sodium cacodylate, 6% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mMsodium cacodylate1droppH6.5
22.5 mMbeta-mercaptoethanol1drop
34 mML-cysteine1drop
42 mMEGTA1drop
520 mg/mlprotein1drop
628 %PEG15001reservoir
730 mMsodium cacodylate1reservoirpH7.0
86 %glycerol1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 14-BM-D111.02046, 0.97997, 0.94286
SYNCHROTRONAPS 14-BM-D21.02046, 0.97997, 0.94286
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 7, 2000Bent cylindrical Si-mirror (Rh coating)
ADSC QUANTUM 42CCDDec 8, 2000Bent cylindrical Si-mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray1
2SI(111) DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.020461
30.979971
40.942861
ReflectionResolution: 1.15→30 Å / Num. all: 27160 / Num. obs: 25759 / % possible obs: 95.2 % / Redundancy: 14.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.7
Reflection shellResolution: 1.15→1.24 Å / Redundancy: 8 % / Rmerge(I) obs: 0.267 / Num. unique all: 4162 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 25856 / % possible obs: 88.2 % / Num. measured all: 399427 / Rmerge(I) obs: 0.061 / Biso Wilson estimate: 14.8 Å2
Reflection shell
*PLUS
Rmerge(I) obs: 0.267

-
Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.15→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1226 5 %RANDOM
Rwork0.186 ---
all0.186 25759 --
obs0.186 24523 95.2 %-
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 0 0 117 826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d2.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d2.07
LS refinement shellResolution: 1.15→1.24 Å / Rfactor Rfree error: 0.09
RfactorNum. reflection% reflection
Rfree0.22 208 -
Rwork0.186 --
obs-4162 87.6 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.07
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.186

+
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