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- PDB-7o4p: Cystal structure of Zymogen Granule Protein 16 (ZG16) -

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Basic information

Entry
Database: PDB / ID: 7o4p
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: 1.08 Å
AuthorsJavitt, G. / 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 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4413
Polymers16,3131
Non-polymers1282
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-12 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.336, 58.336, 82.618
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer (HEPES), pH 7.0, 30 % v/v Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9731 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: 0.9731 Å / Relative weight: 1
ReflectionResolution: 1.08→43.101 Å / Num. obs: 69590 / % possible obs: 99.04 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.67 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03997 / Net I/σ(I): 11.6
Reflection shellResolution: 1.08→1.119 Å / Redundancy: 3 % / Num. unique obs: 6920 / CC1/2: 0.411 / % possible all: 99.58

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APA

3apa


Resolution: 1.08→43.1 Å / SU ML: 0.1592 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 21.5495 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1748 3207 2.57 %
Rwork0.1645 121409 -
obs0.1648 124616 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.25 Å2
Refinement stepCycle: LAST / Resolution: 1.08→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 7 225 1317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651284
X-RAY DIFFRACTIONf_angle_d0.97741771
X-RAY DIFFRACTIONf_chiral_restr0.0784183
X-RAY DIFFRACTIONf_plane_restr0.0063233
X-RAY DIFFRACTIONf_dihedral_angle_d3.1651025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.10.41441370.37395189X-RAY DIFFRACTION90.73
1.1-1.110.38511400.355164X-RAY DIFFRACTION90.9
1.11-1.130.3181320.33145130X-RAY DIFFRACTION90.12
1.13-1.150.3471290.30565141X-RAY DIFFRACTION88.84
1.15-1.170.30491430.29645046X-RAY DIFFRACTION89.1
1.17-1.190.30561450.28745331X-RAY DIFFRACTION92.64
1.19-1.220.26771410.27115330X-RAY DIFFRACTION93.27
1.22-1.250.25761390.26165308X-RAY DIFFRACTION93.48
1.25-1.270.24211410.24945281X-RAY DIFFRACTION91.87
1.27-1.310.21531260.24195175X-RAY DIFFRACTION90.57
1.31-1.340.25081270.22935151X-RAY DIFFRACTION91.13
1.34-1.380.25441400.21475493X-RAY DIFFRACTION95.02
1.38-1.430.21221520.20325468X-RAY DIFFRACTION95.53
1.43-1.480.20571450.18255400X-RAY DIFFRACTION94.72
1.48-1.540.19781430.17525333X-RAY DIFFRACTION92.33
1.54-1.610.18071330.17115168X-RAY DIFFRACTION90.69
1.61-1.690.15491440.1555311X-RAY DIFFRACTION93.97
1.69-1.80.18191410.14545543X-RAY DIFFRACTION96.37
1.8-1.930.13031460.13725483X-RAY DIFFRACTION96.16
1.93-2.130.13811410.12575238X-RAY DIFFRACTION92.09
2.13-2.440.11561400.13085273X-RAY DIFFRACTION91.75
2.44-3.070.13621500.13655370X-RAY DIFFRACTION93.45
3.07-43.10.17291320.14335083X-RAY DIFFRACTION89.28

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