8J8D

Crystal structure of SRCR domain 11 of DMBT1

• PDB DOI: https://doi.org/10.2210/pdb8J8D/pdb

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


• Deposited: 2023-05-01 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: 1.51 Å
• R-Value Free: 0.172 
• R-Value Work: 0.138 
• R-Value Observed: 0.140 

Starting Model: experimental

Literature

Crystal structure of SRCR domain 11 of DMBT1

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

Macromolecule Content

• Total Structure Weight: 12.75 kDa 
• Atom Count: 969 
• Modelled Residue Count: 108 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deleted in malignant brain tumors 1 protein	A	119	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
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.172 
• R-Value Work: 0.138 
• R-Value Observed: 0.140 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.802	α = 90
b = 31.705	β = 90
c = 35.219	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

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary