1VRM | pdb_00001vrm

Crystal structure of the apbe protein (tm1553) from thermotoga maritima msb8 at 1.58 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VRM/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-03-10 Released: 2005-03-22 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 

Literature

Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution.

Han, G.W., Sri Krishna, S., Schwarzenbacher, R., McMullan, D., Ginalski, K., Elsliger, M.A., Brittain, S.M., Abdubek, P., Agarwalla, S., Ambing, E., Astakhova, T., Axelrod, H., Canaves, J.M., Chiu, H.J., DiDonato, M., Grzechnik, S.K., Hale, J., Hampton, E., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Kreusch, A., Kuhn, P., Miller, M.D., Morse, A.T., Moy, K., Nigoghossian, E., Oommachen, S., Ouyang, J., Paulsen, J., Quijano, K., Reyes, R., Rife, C., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Wang, X., West, B., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2006) Proteins 64: 1083-1090

• PubMed: 16779835 
• DOI: https://doi.org/10.1002/prot.20950
• Primary Citation of Related Structures:  
  1VRM

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Organizational Affiliation: 
• Joint Center for Structural Genomics, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.26 kDa 
• Atom Count: 2,895 
• Modeled Residue Count: 309 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1553	A	325	Thermotoga maritima MSB8	Mutation(s): 5  Gene Names: TM1553 EC: 2.7.1.180
UniProt
Find proteins for Q9X1N9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1N9  Go to UniProtKB:  Q9X1N9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
UNL	B [auth A]	Unknown ligand SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 

Diffraction Data: https://doi.org/10.18430/M31VRM

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.742	α = 90
b = 76.946	β = 90
c = 86.587	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-22 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary