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X-ray crystal structure of racemic non-glycosylated chemokine Ser-CCL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

(Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis.

Okamoto, R.Mandal, K.Sawaya, M.R.Kajihara, Y.Yeates, T.O.Kent, S.B.

(2014) Angew.Chem.Int.Ed.Engl. 53: 5194-5198

  • DOI: 10.1002/anie.201400679
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Our goal was to obtain the X-ray crystal structure of the glycosylated chemokine Ser-CCL1. Glycoproteins can be hard to crystallize because of the heterogeneity of the oligosaccharide (glycan) moiety. We used glycosylated Ser-CCL1 that had been prepa ...

    Our goal was to obtain the X-ray crystal structure of the glycosylated chemokine Ser-CCL1. Glycoproteins can be hard to crystallize because of the heterogeneity of the oligosaccharide (glycan) moiety. We used glycosylated Ser-CCL1 that had been prepared by total chemical synthesis as a homogeneous compound containing an N-linked asialo biantennary nonasaccharide glycan moiety of defined covalent structure. Facile crystal formation occurred from a quasi-racemic mixture consisting of glycosylated L-protein and non-glycosylated-D-protein, while no crystals were obtained from the glycosylated L-protein alone. The structure was solved at a resolution of 2.6-2.1 Å. However, the glycan moiety was disordered: only the N-linked GlcNAc sugar was well-defined in the electron density map. A racemic mixture of the protein enantiomers L-Ser-CCL1 and D-Ser-CCL1 was also crystallized, and the structure of the true racemate was solved at a resolution of 2.7-2.15 Å. Superimposition of the structures of the protein moieties of L-Ser-CCL1 and glycosylated-L-Ser-CCL1 revealed there was no significant alteration of the protein structure by N-glycosylation.


    Organizational Affiliation

    Departments of Chemistry: Biochemistry & Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637 (USA); Current address: Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, JAPAN.. skent@uchicago.edu, rokamoto@chem.sci.osaka-u.ac.jp, rokamoto@chem.sci.osaka-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-C motif chemokine 1
A, B
74Homo sapiensMutation(s): 0 
Gene Names: CCL1 (SCYA1)
Find proteins for P22362 (Homo sapiens)
Go to Gene View: CCL1
Go to UniProtKB:  P22362
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-Ser-CCL1
C, D
74N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  19 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DCY
Query on DCY
C, D
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DPR
Query on DPR
C, D
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
C, D
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DHI
Query on DHI
C, D
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
C, D
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
C, D
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
C, D
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
C, D
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
C, D
D-PEPTIDE LINKINGC3 H7 N O2

--

DPN
Query on DPN
C, D
D-PEPTIDE LINKINGC9 H11 N O2

--

DGN
Query on DGN
C, D
D-PEPTIDE LINKINGC5 H10 N2 O3

--

MED
Query on MED
C, D
D-PEPTIDE LINKINGC5 H11 N O2 S

--

DAS
Query on DAS
C, D
D-PEPTIDE LINKINGC4 H7 N O4

--

DSG
Query on DSG
C, D
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DTR
Query on DTR
C, D
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DTY
Query on DTY
C, D
D-PEPTIDE LINKINGC9 H11 N O3

--

DAR
Query on DAR
C, D
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.480α = 109.46
b = 48.860β = 106.84
c = 51.050γ = 109.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
ADSCdata collection
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Database references