5H7N

Crystal structure of human NLRP12-PYD with a MBP tag


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.849 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design of an expression system to enhance MBP-mediated crystallization

Jin, T.C.Chuenchor, W.Jiang, J.Cheng, J.Li, Y.Fang, K.Huang, M.Smith, P.Xiao, T.S.

(2017) Sci Rep 7: 40991-40991

  • DOI: 10.1038/srep40991
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression construct ...

    Crystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression constructs for crystallization of MBP fusion proteins remains a challenge. To increase the success rate of MBP-facilitated crystallization, a series of expression vectors have been designed with either a short flexible linker or a set of rigid helical linkers. Seven death domain superfamily members were tested for crystallization with this set of vectors, six of which had never been crystallized before. All of the seven targets were crystallized, and their structures were determined using at least one of the vectors. Our successful crystallization of all of the targets demonstrates the validity of our approach and expands the arsenal of the crystallization chaperone toolkit, which may be applicable to crystallization of other difficult protein targets, as well as to other crystallization chaperones.


    Organizational Affiliation

    Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NLRP12-PYD with MBP tag
A, B
478Homo sapiensEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 0 
Gene Names: NLRP12 (NALP12, PYPAF7, RNO), malE
Find proteins for P59046 (Homo sapiens)
Go to Gene View: NLRP12
Go to UniProtKB:  P59046
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MTT
Query on MTT

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Download CCD File 
A, B
MALTOTETRAOSE
C24 H42 O21
LUEWUZLMQUOBSB-ZLBHSGTGSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.849 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.540α = 90.00
b = 104.550β = 98.95
c = 110.940γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-11-19 
  • Released Date: 2017-02-15 
  • Deposition Author(s): Jin, T.C., Xiao, T.S.

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release