3L2N | pdb_00003l2n

Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3L2N/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella denitrificans OS217
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-15 Released: 2009-12-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 89.81 kDa 
• Atom Count: 6,156 
• Modeled Residue Count: 752 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M14, carboxypeptidase A	A, B	395	Shewanella denitrificans OS217	Mutation(s): 0  Gene Names: Sden_1905
UniProt
Find proteins for Q12MY8 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12MY8  Go to UniProtKB:  Q12MY8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL	D [auth A], H [auth B]	Unknown ligand BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33L2N

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.417	α = 90
b = 81.417	β = 90
c = 479.685	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary