4WRC | pdb_00004wrc

Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D)

• PDB DOI: https://doi.org/10.2210/pdb4WRC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2014-10-23 Released: 2016-02-10 
• Deposition Author(s): Rynkiewicz, M.J., Wu, H., Cafarella, T.R., Nikolaidis, N.M., Head, J.F., Seaton, B.A., McCormack, F.X.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Differential ligand binding specificities of the pulmonary collectins are determined by the conformational freedom of a surface loop

Rynkiewicz, M.J., Wu, H., Cafarella, T.R., Nikolaidis, N.M., Head, J.F., Seaton, B.A., McCormack, F.X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.87 kDa 
• Atom Count: 1,191 
• Modeled Residue Count: 140 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pulmonary surfactant-associated protein A	A	148	Rattus norvegicus	Mutation(s): 5  Gene Names: Sftpa1, Sftp-1, Sftp1, Sftpa
UniProt
Find proteins for P08427 (Rattus norvegicus) Explore P08427  Go to UniProtKB:  P08427

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	B [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.774	α = 90
b = 68.774	β = 90
c = 168.852	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Rynkiewicz, M.J., Wu, H., Cafarella, T.R., Nikolaidis, N.M., Head, J.F., Seaton, B.A., McCormack, F.X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	#PO1-AI083222

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary