2I7A | pdb_00002i7a

Domain IV of Human Calpain 13

• PDB DOI: https://doi.org/10.2210/pdb2I7A/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-30 Released: 2006-09-12 
• Deposition Author(s): Walker, J.R., Ng, K., Davis, T.L., Ravulapalli, R., Butler-cole, C., Finerty Jr., P.J., Newman, E.M., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structure of Human Calpain 13

Walker, J.R., Ng, K., Davis, T.L., Ravulapalli, R., Butler-Cole, C., Finerty Jr., P.J., Newman, E.M., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 20.45 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 157 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpain 13	A	174	Homo sapiens	Mutation(s): 0  Gene Names: CAPN13 EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q6MZZ7 (Homo sapiens) Explore Q6MZZ7  Go to UniProtKB:  Q6MZZ7
PHAROS:  Q6MZZ7 GTEx:  ENSG00000162949

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.115	α = 90
b = 86.115	β = 90
c = 47.417	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-12 
Deposition Author(s): Walker, J.R., Ng, K., Davis, T.L., Ravulapalli, R., Butler-cole, C., Finerty Jr., P.J., Newman, E.M., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-09-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description