Evidence: NMR relaxation study, Observation of MgF3- transition state analog using 19F-NMR spectroscopy
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
9020 Å2
ΔGint
-44 kcal/mol
Surface area
30110 Å2
Method
PISA
Unit cell
Length a, b, c (Å)
73.765, 66.489, 76.958
Angle α, β, γ (deg.)
90.000, 95.270, 90.000
Int Tables number
4
Space group name H-M
P1211
-
Components
-
Protein , 2 types, 4 molecules ACBD
#1: Protein
RhoGTPase-activatingprotein1 / CDC42 GTPase-activating protein / GTPase-activating protein rhoGAP / Rho-related small GTPase ...CDC42 GTPase-activating protein / GTPase-activating protein rhoGAP / Rho-related small GTPase protein activator / Rho-type GTPase-activating protein 1 / p50-RhoGAP
Mass: 27502.482 Da / Num. of mol.: 2 / Mutation: R85A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP1, CDC42GAP, RHOGAP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07960
#2: Protein
TransformingproteinRhoA / Rho cDNA clone 12 / h12
Mass: 21688.863 Da / Num. of mol.: 2 / Mutation: Y34(F3Y) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61586, small monomeric GTPase
Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0. ...Details: Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0.1 M BisTris-HCl, pH 5.8, PEG3350 26% (w/v).
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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