3SYX | pdb_00003syx

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.

• PDB DOI: https://doi.org/10.2210/pdb3SYX/pdb

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


• Deposited: 2011-07-18 Released: 2011-08-03 
• Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.271 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein.

Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.92 kDa 
• Atom Count: 955 
• Modeled Residue Count: 118 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sprouty-related, EVH1 domain-containing protein 1	A	130	Homo sapiens	Mutation(s): 0  Gene Names: SPRED1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z699 (Homo sapiens) Explore Q7Z699  Go to UniProtKB:  Q7Z699
PHAROS:  Q7Z699 GTEx:  ENSG00000166068

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YT3	B [auth A]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.271 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.754	α = 90
b = 52.754	β = 90
c = 121.638	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description