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- PDB-5v6k: Crystal Structure of the Second beta-Prism Domain of RbmC from V.... -

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Basic information

Entry
Database: PDB / ID: 5v6k
TitleCrystal Structure of the Second beta-Prism Domain of RbmC from V. cholerae Bound to N-acetylglucosaminyl-beta-1,2-mannose
ComponentsHemolysin-related protein
KeywordsSUGAR BINDING PROTEIN / lectin / beta-prism / glycan-binding domain / N-acetylglucosaminyl-beta-1 / 2-mannose
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 O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
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 31, 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_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

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Assembly

Deposited unit
A: Hemolysin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4083
Polymers14,9331
Non-polymers4752
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.940, 38.770, 51.890
Angle α, β, γ (deg.)90.000, 105.260, 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 O1 biovar El Tor str. 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.04 Å3/Da / Density % sol: 39.57 % / Mosaicity: 0.71 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 2 M sodium sulfate, 1 mM N-acetylglucosaminyl-beta-1,2-mannose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→38.77 Å / Num. obs: 10585 / % possible obs: 91.9 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Net I/σ(I): 11.4 / Num. measured all: 41463 / Scaling rejects: 114
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.477 / Num. measured all: 805 / Num. unique obs: 321 / CC1/2: 0.704 / Rpim(I) all: 0.37 / Rrim(I) all: 0.608 / Net I/σ(I) obs: 1.8 / % possible all: 47.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
MOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XEZ

1xez


Resolution: 1.8→30.652 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 487 4.61 %
Rwork0.1656 10078 -
obs0.1667 10565 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.33 Å2 / Biso mean: 16.8869 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.8→30.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 64 215 1317
Biso mean--18.93 24.65 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031093
X-RAY DIFFRACTIONf_angle_d0.5861488
X-RAY DIFFRACTIONf_chiral_restr0.05173
X-RAY DIFFRACTIONf_plane_restr0.003185
X-RAY DIFFRACTIONf_dihedral_angle_d10.012623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8004-2.06090.18931420.17162724286675
2.0609-2.59630.19961870.16936303817100
2.5963-30.65680.18311580.162237243882100

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