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- PDB-5v6f: Crystal Structure of the Second beta-Prism Domain of RbmC from V.... -

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Basic information

Entry
Database: PDB / ID: 5v6f
TitleCrystal Structure of the Second beta-Prism Domain of RbmC from V. cholerae bound to Mannotriose
ComponentsHemolysin-related protein
KeywordsSUGAR BINDING PROTEIN / lectin / beta-prism / glycan-binding domain / mannotriose
Function / homology
Function and homology information


Metalloprotease StcE, C-terminal / Beta/Gamma crystallin / Hemolysin, beta-prism lectin / Beta-prism lectin / FG-GAP-like repeat / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / FG-GAP repeat ...Metalloprotease StcE, C-terminal / Beta/Gamma crystallin / Hemolysin, beta-prism lectin / Beta-prism lectin / FG-GAP-like repeat / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / FG-GAP repeat / Integrin alpha, N-terminal / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Beta
Similarity search - Domain/homology
Hemolysin-related protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsapo form
AuthorsDe, S. / Kaus, K. / Sinclair, S. / Case, B.C. / Olson, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15 AI101977 United States
CitationJournal: PLoS Pathog. / Year: 2018
Title: Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins.
Authors: De, S. / Kaus, K. / Sinclair, S. / Case, B.C. / Olson, R.
History
DepositionMar 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6294
Polymers14,9331
Non-polymers6973
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer by size exclusion
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.882, 38.581, 50.954
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemolysin-related protein


Mass: 14932.883 Da / Num. of mol.: 1 / Fragment: lectin domain, UNP residues 823-957
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_0930 / Plasmid: pNGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 Express / References: UniProt: Q9KTH2
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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 Å3/Da / Density % sol: 38.44 % / Mosaicity: 0.83 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 2 M sodium sulfate, 2 mM mannotriose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→16.112 Å / Num. obs: 18634 / % possible obs: 95.1 % / Redundancy: 2.6 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.097 / Rsym value: 0.078 / Net I/av σ(I): 7.5 / Net I/σ(I): 7.7 / Num. measured all: 48096
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.581.80.4811.4441124420.4270.6470.4811.586.1
1.58-1.681.90.3222.2467624980.2840.4320.322292.2
1.68-1.7920.2263.1480824340.1980.3020.2262.696.5
1.79-1.942.10.154481823130.1310.20.153.898.2
1.94-2.122.30.1115.3486521350.0910.1450.1115.698.2
2.12-2.372.80.0976537219210.0680.1190.0977.697.6
2.37-2.743.20.0798.1531016680.050.0940.0799.696.3
2.74-3.354.10.05111.5585814440.0280.0580.05116.897.3
3.35-4.744.60.0413.9524911510.0210.0450.043099.8
4.74-16.1124.30.0331327296280.0180.0380.03329.295.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å16.11 Å
Translation1.5 Å16.11 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XEZ

1xez


Resolution: 1.5→16.112 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 1862 10 %
Rwork0.1635 16755 -
obs0.1664 18617 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.16 Å2 / Biso mean: 9.2837 Å2 / Biso min: 1.09 Å2
Refinement stepCycle: final / Resolution: 1.5→16.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 76 237 1355
Biso mean--9.84 22.76 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041109
X-RAY DIFFRACTIONf_angle_d0.6631514
X-RAY DIFFRACTIONf_chiral_restr0.052178
X-RAY DIFFRACTIONf_plane_restr0.003185
X-RAY DIFFRACTIONf_dihedral_angle_d9.552638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.54060.30161260.27591137126385
1.5406-1.58590.30291330.24051195132888
1.5859-1.6370.24411340.22311209134391
1.637-1.69550.23461430.20211285142894
1.6955-1.76330.21911450.191304144996
1.7633-1.84340.21481450.16731303144898
1.8434-1.94050.20661470.15411327147498
1.9405-2.06180.17921470.14271326147398
2.0618-2.22060.17481480.13741323147198
2.2206-2.44340.16821470.14091320146797
2.4434-2.79540.18251450.14561303144896
2.7954-3.51590.14131490.13561344149398
3.5159-16.1130.17451530.15941379153299

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