3RM1 | pdb_00003rm1

1.24 Angstrom X-ray structure of bovine TRTK12-Ca(2+)-S100B D63N

• PDB DOI: https://doi.org/10.2210/pdb3RM1/pdb

• Classification: METAL BINDING PROTEIN/PROTEIN BINDING
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-04-20 Released: 2012-04-25 
• Deposition Author(s): Liriano, M.A., Weber, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.223 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

The effects of CapZ peptide (TRTK12) on the protein dynamics of S100B and S100B D63N

Liriano, M.A., Varney, K.M., Inman, K.G., Ishima, R., Weber, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.89 kDa 
• Atom Count: 894 
• Modeled Residue Count: 98 
• Deposited Residue Count: 101 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-B	A	92	Bos taurus	Mutation(s): 1  Gene Names: S100B
UniProt
Find proteins for P02638 (Bos taurus) Explore P02638  Go to UniProtKB:  P02638

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-capping protein subunit alpha-2	B	9	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q5E997 (Bos taurus) Explore Q5E997  Go to UniProtKB:  Q5E997

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.223 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.007	α = 90
b = 89.251	β = 90
c = 59.668	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Liriano, M.A., Weber, D.J.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description