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- PDB-7c0n: Crystal structure of a self-assembling galactosylated peptide hom... -

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Basic information

Entry
Database: PDB / ID: 7c0n
TitleCrystal structure of a self-assembling galactosylated peptide homodimer
ComponentsSelf-assembling galactosylated tyrosine-rich peptide
KeywordsDE NOVO PROTEIN / Self-assembling glycopeptide / tyrosine-rich peptide / O-glycan modification.
Function / homologybeta-D-galactopyranose
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.552 Å
AuthorsHe, C. / Wu, S. / Chi, C. / Zhang, W. / Ma, M. / Lai, L. / Dong, S.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507602 China
Ministry of Science and Technology (MoST, China)2019ZX09301-106 China
National Natural Science Foundation of China (NSFC)21822701 China
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Glycopeptide Self-Assembly Modulated by Glycan Stereochemistry through Glycan-Aromatic Interactions.
Authors: He, C. / Wu, S. / Liu, D. / Chi, C. / Zhang, W. / Ma, M. / Lai, L. / Dong, S.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Self-assembling galactosylated tyrosine-rich peptide
B: Self-assembling galactosylated tyrosine-rich peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0045
Polymers1,5482
Non-polymers4563
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, The assembly provided by liquid chromatography-mass spectrometry (LC-MS) is monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-16 kcal/mol
Surface area1690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.837, 72.837, 72.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+1/4
#3: x+1/4,z+1/4,-y+1/4
#4: z+1/4,y+1/4,-x+1/4
#5: -z+1/4,y+1/4,x+1/4
#6: -y+1/4,x+1/4,z+1/4
#7: y+1/4,-x+1/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y+1/4,x+1/4,-z+1/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+1/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x,y+1/2,z+1/2
#26: x+1/4,-z+3/4,y+3/4
#27: x+1/4,z+3/4,-y+3/4
#28: z+1/4,y+3/4,-x+3/4
#29: -z+1/4,y+3/4,x+3/4
#30: -y+1/4,x+3/4,z+3/4
#31: y+1/4,-x+3/4,z+3/4
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y+1/4,x+3/4,-z+3/4
#44: -y+1/4,-x+3/4,-z+3/4
#45: z+1/4,-y+3/4,x+3/4
#46: -z+1/4,-y+3/4,-x+3/4
#47: -x+1/4,z+3/4,y+3/4
#48: -x+1/4,-z+3/4,-y+3/4
#49: x+1/2,y,z+1/2
#50: x+3/4,-z+1/4,y+3/4
#51: x+3/4,z+1/4,-y+3/4
#52: z+3/4,y+1/4,-x+3/4
#53: -z+3/4,y+1/4,x+3/4
#54: -y+3/4,x+1/4,z+3/4
#55: y+3/4,-x+1/4,z+3/4
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+3/4,x+1/4,-z+3/4
#68: -y+3/4,-x+1/4,-z+3/4
#69: z+3/4,-y+1/4,x+3/4
#70: -z+3/4,-y+1/4,-x+3/4
#71: -x+3/4,z+1/4,y+3/4
#72: -x+3/4,-z+1/4,-y+3/4
#73: x+1/2,y+1/2,z
#74: x+3/4,-z+3/4,y+1/4
#75: x+3/4,z+3/4,-y+1/4
#76: z+3/4,y+3/4,-x+1/4
#77: -z+3/4,y+3/4,x+1/4
#78: -y+3/4,x+3/4,z+1/4
#79: y+3/4,-x+3/4,z+1/4
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+3/4,x+3/4,-z+1/4
#92: -y+3/4,-x+3/4,-z+1/4
#93: z+3/4,-y+3/4,x+1/4
#94: -z+3/4,-y+3/4,-x+1/4
#95: -x+3/4,z+3/4,y+1/4
#96: -x+3/4,-z+3/4,-y+1/4

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Components

#1: Protein/peptide Self-assembling galactosylated tyrosine-rich peptide


Mass: 773.853 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40%(w/v) PEG 1000, 0.1 M Sodium phosphate dibasic/Citric acid(pH 4.2), 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1.54191 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54191 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 2694 / % possible obs: 100 % / Redundancy: 72.6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 54.2
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 63 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 17 / Num. unique obs: 256 / Rsym value: 0.369

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.552→25.752 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2495 118 4.4 %
Rwork0.2344 --
obs-2682 100 %
Displacement parametersBiso max: 52.98 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.552→25.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms107 0 50 3 160
Biso mean--26.31 24.37 -
Num. residues----10
LS refinement shellResolution: 1.552→1.607 Å
RfactorNum. reflection% reflection
Rfree0.2328 --
Rwork0.2326 255 -
obs--100 %

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