2PNW | pdb_00002pnw

Crystal structure of membrane-bound lytic murein transglycosylase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2PNW/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-25 Released: 2007-05-08 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of membrane-bound lytic murein transglycosylase from Agrobacterium tumefaciens.

Bonanno, J.B., Dickey, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.42 kDa 
• Atom Count: 3,185 
• Modeled Residue Count: 354 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-bound lytic murein transglycosylase	A	380	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: mltA, AGR_C_15, Atu0009
UniProt
Find proteins for A9CKT8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CKT8  Go to UniProtKB:  A9CKT8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.665	α = 90
b = 88.665	β = 90
c = 221.434	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
CCP4	data scaling
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-02-21
  Changes: Data collection, Database references