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PDBsum entry 2cl0
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protein ligands metals links
Nucleotide binding protein PDB id
2cl0

 

 

 

 

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Contents
Protein chain
166 a.a. *
Ligands
TRS
GNP
XY2
Metals
_MG ×5
Waters ×168
* Residue conservation analysis
PDB id:
2cl0
Name: Nucleotide binding protein
Title: Crystal structure analysis of a fluorescent form of h-ras p21 in complex with gppnhp
Structure: Gtpase hras. Chain: x. Fragment: residues 1-166. Synonym: transforming protein p21, p21ras, h-ras-1, c-h-ras. Engineered: yes. Mutation: yes. Other_details: ianbd fluorophore was attached to cys-32
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.148     R-free:   0.185
Authors: B.U.Klink,R.S.Goody,A.J.Scheidig
Key ref: B.U.Klink et al. (2006). A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction. Biophys J, 91, 981-992. PubMed id: 16698776
Date:
25-Apr-06     Release date:   31-May-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas from Homo sapiens
Seq:
Struc: 		189 a.a.
166 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.6.5.2  - small monomeric GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 =
GDP
Bound ligand (Het Group name = GNP)
matches with 81.82% similarity 		+ phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Biophys J 91:981-992 (2006)
PubMed id: 16698776  
 
 
A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction.
B.U.Klink, R.S.Goody, A.J.Scheidig.
 
  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. 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20949621 L.Gremer, T.Merbitz-Zahradnik, R.Dvorsky, I.C.Cirstea, C.P.Kratz, M.Zenker, A.Wittinghofer, and M.R.Ahmadian (2011).
Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders.
  Hum Mutat, 32, 33-43.  
20973973 B.U.Klink, and A.J.Scheidig (2010).
New insight into the dynamic properties and the active site architecture of H-Ras p21 revealed by X-ray crystallography at very high resolution.
  BMC Struct Biol, 10, 38.  
19240328 J.McGeehan, R.B.Ravelli, J.W.Murray, R.L.Owen, F.Cipriani, S.McSweeney, M.Weik, and E.F.Garman (2009).
Colouring cryo-cooled crystals: online microspectrophotometry.
  J Synchrotron Radiat, 16, 163-172.  
19240329 R.L.Owen, A.R.Pearson, A.Meents, P.Boehler, V.Thominet, and C.Schulze-Briese (2009).
A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source.
  J Synchrotron Radiat, 16, 173-182.  
18547521 A.A.Gorfe, B.J.Grant, and J.A.McCammon (2008).
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.
  Structure, 16, 885-896.  
18768811 B.Barstow, N.Ando, C.U.Kim, and S.M.Gruner (2008).
Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.
  Proc Natl Acad Sci U S A, 105, 13362-13366.
PDB codes: 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu
17959373 T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.
  Curr Opin Struct Biol, 17, 580-586.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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