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- PDB-4gx7: Vibrio Cholerae Cytolysin Beta-Prism Domain With Methyl-Alpha-Man... -

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Basic information

Entry
Database: PDB / ID: 4gx7
TitleVibrio Cholerae Cytolysin Beta-Prism Domain With Methyl-Alpha-Mannose Bound
ComponentsCytolysin and hemolysin HlyA Pore-forming toxin
KeywordsTOXIN / lectin / carbohydrate-binding domain / beta-prism / pore-forming toxin / hemolysin / cytolysin / glycan-binding
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / carbohydrate binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / host cell plasma membrane ...cytolysis in another organism / toxin activity / carbohydrate binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Jacalin-like lectin domain ...Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Large ribosomal subunit protein uL5 / Hemolysin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsLevan, S. / Olson, R.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Vibrio cholerae Cytolysin Recognizes the Heptasaccharide Core of Complex N-Glycans with Nanomolar Affinity.
Authors: Levan, S. / De, S. / Olson, R.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Jul 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_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Cytolysin and hemolysin HlyA Pore-forming toxin
B: Cytolysin and hemolysin HlyA Pore-forming toxin
C: Cytolysin and hemolysin HlyA Pore-forming toxin
D: Cytolysin and hemolysin HlyA Pore-forming toxin
E: Cytolysin and hemolysin HlyA Pore-forming toxin
F: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,97112
Polymers97,8066
Non-polymers1,1656
Water00
1
A: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,3011
Non-polymers1941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,3011
Non-polymers1941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,3011
Non-polymers1941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,3011
Non-polymers1941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,3011
Non-polymers1941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytolysin and hemolysin HlyA Pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4952
Polymers16,3011
Non-polymers1941
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.770, 99.770, 172.366
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Cytolysin and hemolysin HlyA Pore-forming toxin


Mass: 16301.008 Da / Num. of mol.: 6 / Fragment: Carbohydrate-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 12129(1) / Gene: HlyA, VCG_000884 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: C2C744, UniProt: P09545*PLUS
#2: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M Bis-tris, 25% PEG 3350, 30 mM Me-alpha-mannose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→24.895 Å / Num. all: 23789 / Num. obs: 23789 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rsym value: 0.211 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.85-34.90.4771.51680934010.477100
3-3.194.90.4231.71606232470.423100
3.19-3.414.90.2992.41510030520.299100
3.41-3.684.90.23831419828690.238100
3.68-4.034.90.1873.71295626220.187100
4.03-4.514.90.1384.81185624140.138100
4.51-5.24.90.1155.61038021280.115100
5.2-6.374.80.1096.6876818210.109100
6.37-9.014.70.0799.3679414500.07999.9
9.01-24.8954.10.04515.632247850.04594.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å24.89 Å
Translation2.7 Å24.89 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1XEZ (Residues 585-716)

1xez


Resolution: 2.85→24.895 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.847 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1182 4.97 %RANDOM
Rwork0.1946 ---
obs0.1973 23763 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.06 Å2 / Biso mean: 24.7374 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.85→24.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 78 0 5853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055942
X-RAY DIFFRACTIONf_angle_d1.0458085
X-RAY DIFFRACTIONf_chiral_restr0.058942
X-RAY DIFFRACTIONf_plane_restr0.0041058
X-RAY DIFFRACTIONf_dihedral_angle_d14.3921995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-2.97960.30751440.241727772921
2.9796-3.13640.30271420.242827752917
3.1364-3.33240.28751590.220827772936
3.3324-3.5890.27451350.198228022937
3.589-3.94890.25061550.180527962951
3.9489-4.51740.20131530.163128232976
4.5174-5.68030.19831360.161728632999
5.6803-24.89570.22691580.201329683126

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