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- PDB-3vzg: Crystal structure of human pancreatic secretory protein ZG16p wit... -

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Basic information

Entry
Database: PDB / ID: 3vzg
TitleCrystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine
ComponentsZymogen granule membrane protein 16
KeywordsSUGAR BINDING PROTEIN / beta-prism fold
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 / collagen-containing extracellular matrix / defense response to Gram-positive bacterium / extracellular space
Similarity search - Function
: / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / THREONINE / Zymogen granule membrane protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKanagawa, M. / Yamaguchi, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin
Authors: Kanagawa, M. / Liu, Y. / Hanashima, S. / Ikeda, A. / Chai, W. / Nakano, Y. / Kojima-Aikawa, K. / Feizi, T. / Yamaguchi, Y.
History
DepositionOct 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,8725
Polymers15,5011
Non-polymers3704
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.397, 73.022, 30.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 15501.401 Da / Num. of mol.: 1 / Fragment: UNP residues 21-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZG16 / Plasmid: pCold-I(MBP fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21(DE3) / References: UniProt: O60844
#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 0.09M MES(pH 6.5), 0.09M Sodium phosphate, 0.09M Potassium phosphate, 1.8M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 3909 / % possible obs: 98.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APA

3apa


Resolution: 2.7→45.6 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.832 / SU B: 13.276 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 170 4.4 %RANDOM
Rwork0.217 ---
obs0.22 3660 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---0.9 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 21 51 1156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211131
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8271.9611529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6325137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4112250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95615179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.706159
X-RAY DIFFRACTIONr_chiral_restr0.0470.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02861
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.140.2441
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2748
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.040.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1291.5698
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.23821085
X-RAY DIFFRACTIONr_scbond_it0.2213506
X-RAY DIFFRACTIONr_scangle_it0.3924.5444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 10 -
Rwork0.276 268 -
obs--97.54 %

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