8J8T | pdb_00008j8t

Crystal structure of calcium-saturated SRCR domain 11 of DMBT1

• PDB DOI: https://doi.org/10.2210/pdb8J8T/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-02 Released: 2023-12-13 
• Deposition Author(s): Zhang, C., Lu, P., Nagata, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Calcium-saturated SRCR domain 11 of SALSA

Zhang, C., Lu, P., Nagata, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.86 kDa 
• Atom Count: 1,946 
• Modeled Residue Count: 228 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deleted in malignant brain tumors 1 protein	A, B	120	Homo sapiens	Mutation(s): 0  Gene Names: DMBT1, GP340
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGM3 (Homo sapiens) Explore Q9UGM3  Go to UniProtKB:  Q9UGM3
PHAROS:  Q9UGM3 GTEx:  ENSG00000187908

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.197	α = 90
b = 47.305	β = 101.85
c = 69.833	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Zhang, C., Lu, P., Nagata, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H02151
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05771
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H03045

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary