PDBsum entry 1vrm

Go to PDB code: 
protein ligands links
Biosynthetic protein PDB id
Protein chain
309 a.a. *
MPD ×2
Waters ×404
* Residue conservation analysis
PDB id:
Name: Biosynthetic protein
Title: Crystal structure of the apbe protein (tm1553) from thermoto maritima msb8 at 1.58 a resolution
Structure: Hypothetical protein tm1553. Chain: a. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm1553. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.58Å     R-factor:   0.157     R-free:   0.191
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
G.W.Han et al. (2006). Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution. Proteins, 64, 1083-1090. PubMed id: 16779835 DOI: 10.1002/prot.20950
10-Mar-05     Release date:   22-Mar-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9X1N9  (Q9X1N9_THEMA) -  Uncharacterized protein
352 a.a.
309 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein flavinylation   1 term 


DOI no: 10.1002/prot.20950 Proteins 64:1083-1090 (2006)
PubMed id: 16779835  
Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution.
G.W.Han, S.Sri Krishna, R.Schwarzenbacher, D.McMullan, K.Ginalski, M.A.Elsliger, S.M.Brittain, P.Abdubek, S.Agarwalla, E.Ambing, T.Astakhova, H.Axelrod, J.M.Canaves, H.J.Chiu, M.DiDonato, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, E.Koesema, A.Kreusch, P.Kuhn, M.D.Miller, A.T.Morse, K.Moy, E.Nigoghossian, S.Oommachen, J.Ouyang, J.Paulsen, K.Quijano, R.Reyes, C.Rife, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, X.Wang, B.West, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of TM1553. A: Ribbon drawing where the N-terminal domain (cyan), helical domain (pink), linker region (slate-blue), and C-terminal domain (yellow) are colored to illustrate the domain organization. Helices (H1-H12) and -strands ( 1- 15) are labeled, and the unknown ligand is represented as orange spheres. B: Diagram showing the secondary structural elements in TM1553 superimposed on its primary sequence. The -helices, 3[10]-helices, -strands (indicated by red A, B, C, and D to represent the -sheet designation), -bulges, and -turns are indicated. The -hairpins are depicted as red loops. Dashed lines indicate that no electron density was observed for that region.
Figure 2.
Figure 2. A: Structural diagram of the monomeric unit of uricase (PDB 1r51), which is also composed of a tandem duplication of the T-fold. The N- and C-terminal domains are colored green and gray, respectively. B: Tunnel-shaped oligomeric complex of uricase. The active site is composed of residues from different subunits (colored gray, beige, green, and slate-blue) of the enzyme. The ligand molecules bound at the active sites are shown in CPK. C: Stereo diagram of the structure alignment of the monomeric unit of uricase and TM1553. TM1553 is colored blue and uricase gray. Uricase does not contain the additional helical domain. The ligands at the active sites of uricase (shown in CPK) and TM1553 (shown as orange spheres) are in completely different locations. D: Stereo diagram of the putative active site of TM1553. The structure of TM1553 is colored gray and the side-chains of residues within a 4 Å shell of the UNL are displayed in ball-and-stick representation. The electron density of a 2Fo-Fc omit map contoured at 1 (blue) around the UNL (orange spheres) in the active site is shown. Water molecules in the active site are not displayed.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 64, 1083-1090) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19465773 T.C.Terwilliger, P.D.Adams, R.J.Read, A.J.McCoy, N.W.Moriarty, R.W.Grosse-Kunstleve, P.V.Afonine, P.H.Zwart, and L.W.Hung (2009).
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
  Acta Crystallogr D Biol Crystallogr, 65, 582-601.  
18369189 C.J.McCleverty, L.Columbus, A.Kreusch, and S.A.Lesley (2008).
Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634.
  Protein Sci, 17, 869-877.
PDB codes: 2vkj 2vko
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.