1J6U | pdb_00001j6u

Crystal structure of UDP-N-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1J6U/pdb

• Classification: LIGASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-08-29 Released: 2002-11-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.279 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution.

Spraggon, G., Schwarzenbacher, R., Kreusch, A., Lee, C.C., Abdubek, P., Ambing, E., Biorac, T., Brinen, L.S., Canaves, J.M., Cambell, J., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Eshagi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Hampton, E., Jaroszewski, L., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kuhn, P., Levin, I., McMullan, D., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Quijano, K., Robb, A., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., von Delft, F., Wang, X., West, B., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Lesley, S.A., Wilson, I.A.

(2004) Proteins 55: 1078-1081

• PubMed: 15146505 
• DOI: https://doi.org/10.1002/prot.20034
• Primary Citation Related Structures: 
  1J6U

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Organizational Affiliation: 
• The Joint Center for Structural Genomics, San Diego, California 92121, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.83 kDa 
• Atom Count: 3,694 
• Modeled Residue Count: 430 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramate-alanine ligase MurC	A	469	Thermotoga maritima	Mutation(s): 8  Gene Names: TM0231 EC: 6.3.2.8
UniProt
Find proteins for Q9WY73 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WY73  Go to UniProtKB:  Q9WY73

Small Molecules

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: 2.30 Å
• R-Value Free:  0.279 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 244.11	α = 90
b = 244.11	β = 90
c = 244.11	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
CCP4	data reduction
SCALEPACK	data scaling
SnB	phasing
MLPHARE	phasing
CCP4	model building
SOLVE	phasing
CNS	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2002-11-06
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2018-07-18
  Changes: Data collection, Database references
• Version 1.5: 2023-01-25
  Changes: Advisory, Database references, Derived calculations
• Version 1.6: 2024-11-13
  Changes: Data collection, Structure summary