3FDG | pdb_00003fdg

The crystal structure of the dipeptidase AC, Metallo peptidase. MEROPS family M19

• PDB DOI: https://doi.org/10.2210/pdb3FDG/pdb

• Classification: HYDROLASE
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-25 Released: 2008-12-23 
• Deposition Author(s): Zhang, R., Hatzos, C., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

The crystal structure of the dipeptidase AC, Metallo peptidase. MEROPS family M19

Zhang, R., Hatzos, C., Freeman, L., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 78.17 kDa 
• Atom Count: 5,748 
• Modeled Residue Count: 686 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidase AC. Metallo peptidase. MEROPS family M19	A, B	355	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: GI:77388796, RHOS4_24130, RSP_0802 EC: 3.4.13.19
UniProt
Find proteins for Q3IZQ3 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IZQ3  Go to UniProtKB:  Q3IZQ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.246	α = 82.42
b = 50.683	β = 73.61
c = 81.594	γ = 68.18

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Zhang, R., Hatzos, C., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations