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- PDB-7o88: Cystal structure of Zymogen Granule Protein 16 (ZG16) -

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Basic information

Entry
Database: PDB / ID: 7o88
TitleCystal structure of Zymogen Granule Protein 16 (ZG16)
ComponentsZymogen granule membrane protein 16
KeywordsSUGAR BINDING PROTEIN / Beta prism / greek key
Function / homology
Function and homology information


suppression of symbiont entry into host / mucus layer / zymogen granule membrane / peptidoglycan binding / Golgi lumen / protein transport / : / carbohydrate binding / defense response to Gram-positive bacterium
Similarity search - Function
: / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
Zymogen granule membrane protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJavitt, G. / Kinzel, A. / Fass, D.
CitationJournal: Febs J. / Year: 2021
Title: Conformational switches and redox properties of the colon cancer-associated human lectin ZG16.
Authors: Javitt, G. / Kinzel, A. / Reznik, N. / Fass, D.
History
DepositionApr 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zymogen granule membrane protein 16
B: Zymogen granule membrane protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8114
Polymers32,6272
Non-polymers1842
Water8,665481
1
A: Zymogen granule membrane protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4052
Polymers16,3131
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zymogen granule membrane protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4052
Polymers16,3131
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.978, 45.418, 146.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zymogen granule membrane protein 16 / Zymogen granule protein 16 / hZG16 / Secretory lectin ZG16


Mass: 16313.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZG16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60844
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium thiocyanate, 20 % w/v polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.2→43.388 Å / Num. obs: 92432 / % possible obs: 97.31 % / Redundancy: 3.7 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08244 / Rpim(I) all: 0.04535 / Net I/σ(I): 8.01
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 3.5 % / Num. unique obs: 8866 / CC1/2: 0.503 / % possible all: 94.98

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APA

3apa


Resolution: 1.2→43.388 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.25 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 1784 1.06 %
Rwork0.1734 166634 -
obs0.1736 92432 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.32 Å2 / Biso mean: 19.0506 Å2 / Biso min: 7.69 Å2
Refinement stepCycle: final / Resolution: 1.2→43.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 18 496 2705
Biso mean--16.78 32.47 -
Num. residues----284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.23250.33831330.32551231289
1.2325-1.26870.31411380.30331324796
1.2687-1.30970.2881370.29371319596
1.3097-1.35650.32821370.27481311795
1.3565-1.41080.27271350.25881314295
1.4108-1.4750.27261420.23761322596
1.475-1.55280.2391400.22231311695
1.5528-1.65010.21921430.19031281993
1.6501-1.77750.19911450.1691306394
1.7775-1.95640.15441360.15591276092
1.9564-2.23940.17381370.14031251291
2.2394-2.82140.17221300.14561230989
2.8214-43.3880.14841310.1381181786

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