2EVW

Crystal structure analysis of a fluorescent form of H-Ras p21 in complex with R-caged GTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction.

Klink, B.U., Goody, R.S., Scheidig, A.J.

(2006) Biophys J 91: 981-992

  • DOI: 10.1529/biophysj.105.078931
  • Primary Citation of Related Structures:  
    2CE2, 2CL0, 2CL6, 2CL7, 2CLC, 2CLD, 2EVW

  • PubMed Abstract: 

    • We present a new design for a fluorescence microspectrophotometer for use in kinetic crystallography in combination with x-ray diffraction experiments. The FLUMIX device (Fluorescence spectroscopy to monitor intermediates in x-ray crystallography) is built for 0 degrees fluorescence detection, which has several advantages in comparison to a conventional fluorometer with 90 degrees design ...

    We present a new design for a fluorescence microspectrophotometer for use in kinetic crystallography in combination with x-ray diffraction experiments. The FLUMIX device (Fluorescence spectroscopy to monitor intermediates in x-ray crystallography) is built for 0 degrees fluorescence detection, which has several advantages in comparison to a conventional fluorometer with 90 degrees design. Due to the reduced spatial requirements and the need for only one objective, the system is highly versatile, easy to handle, and can be used for many different applications. In combination with a conventional stereomicroscope, fluorescence measurements or reaction initiation can be performed directly in a hanging drop crystallization setup. The FLUMIX device can be combined with most x-ray sources, normally without the need of a specialized mechanical support. As a biological model system, we have used H-Ras p21 with an artificially introduced photo-labile GTP precursor (caged GTP) and a covalently attached fluorophore (IANBD amide). Using the FLUMIX system, detailed information about the state of photolyzed crystals of the modified H-Ras p21 (p21(mod)) could be obtained. Measurements in combination with a synchrotron beamline showed significant fluorescence changes in p21(mod) crystals even within a few seconds of x-ray exposure at 100 K.

    Organizational Affiliation: 

    Max-Planck-Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, D-44225 Dortmund, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase HRasA [auth X]166Homo sapiensMutation(s): 2 
Gene Names: HRAS, HRAS1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAG
Query on CAG
Download Ideal Coordinates CCD File 
C [auth X]GUANOSINE 5'-TRIPHOSPHATE P3-[1-(2-NITROPHENYL)ETHYL ESTER]
C18 H23 N6 O16 P3
NYWDUFBXCCSYMK-JPDTYCKISA-N		 Ligand Interaction
XY2
Query on XY2
Download Ideal Coordinates CCD File 
D [auth X]N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NITROBENZ-2-OXA-1,3-DIAZOL-4-YL)ETHYLENEDIAMINE
C12 H15 N5 O4
YSVJZZZGPPWEIC-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth X]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.3α = 90
b = 69.3β = 90
c = 35.51γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2005-11-01 
  • Released Date: 2006-05-30 
    • Deposition Author(s): Klink, B.U.

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations