4XED | pdb_00004xed

PKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20

• PDB DOI: https://doi.org/10.2210/pdb4XED/pdb

• Classification: PROTEIN BINDING
• Organism(s): Thermoplasmatales archaeon SCGC AB-540-F20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-23 Released: 2015-05-13 
• Deposition Author(s): Michalska, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

PKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20

Michalska, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by (software)

Macromolecule Content 

• Total Structure Weight: 11.26 kDa 
• Atom Count: 962 
• Modeled Residue Count: 97 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M14, carboxypeptidase A	A	99	Thermoplasmatales archaeon SCGC AB-540-F20	Mutation(s): 0  Gene Names: MBGDF03_00742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-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: 1.23 Å
• R-Value Free:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34XED

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.186	α = 90
b = 48.869	β = 90
c = 78.509	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing
HKL-3000	data scaling
SBC-Collect	data collection
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP	model building
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Michalska, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Advisory, Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary