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- PDB-4tsm: MBP-fusion protein of PilA1 from C. difficile R20291 residues 26-166 -

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Basic information

Entry
Database: PDB / ID: 4tsm
TitleMBP-fusion protein of PilA1 from C. difficile R20291 residues 26-166
Componentsmaltose-binding protein, pilin chimera
KeywordsCELL ADHESION / Pilin / T4P / fusion
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...protein secretion by the type II secretion system / type II protein secretion system complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / membrane => GO:0016020 / periplasmic space / DNA damage response / membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotetraose / trimethylamine oxide / Pilin / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Peptoclostridium difficile R20291 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsPiepenbrink, K.H. / Sundberg, E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI 110045 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI105881 United States
CitationJournal: Structure / Year: 2015
Title: Structural and Evolutionary Analyses Show Unique Stabilization Strategies in the Type IV Pili of Clostridium difficile.
Authors: Piepenbrink, K.H. / Maldarelli, G.A. / Martinez de la Pena, C.F. / Dingle, T.C. / Mulvey, G.L. / Lee, A. / von Rosenvinge, E. / Armstrong, G.D. / Donnenberg, M.S. / Sundberg, E.J.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Feb 18, 2015Group: Refinement description
Revision 1.4Mar 4, 2015Group: Structure summary
Revision 1.5Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.6Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.7Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / refine / refine_hist / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _refine.pdbx_diffrn_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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: maltose-binding protein, pilin chimera
B: maltose-binding protein, pilin chimera
C: maltose-binding protein, pilin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,56825
Polymers169,1423
Non-polymers3,42722
Water14,358797
1
A: maltose-binding protein, pilin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,64810
Polymers56,3811
Non-polymers1,2679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: maltose-binding protein, pilin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4237
Polymers56,3811
Non-polymers1,0426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: maltose-binding protein, pilin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4988
Polymers56,3811
Non-polymers1,1177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.951, 79.366, 164.746
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1333-

HOH

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Components

#1: Protein maltose-binding protein, pilin chimera / MBP / Mmbp / PilA1


Mass: 56380.512 Da / Num. of mol.: 3
Fragment: UNP residues 27-392 (MBP), UNP residues 35-173 (PilA1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Peptoclostridium difficile R20291 (bacteria)
Gene: malE, HMPREF9530_03068, CDR20291_3350 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: D8A942, UniProt: C9YRY2, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H9NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG2000 MME, 0.2 M trimethylamine N-oxide, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 99.1 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.899→38.58 Å / Num. all: 146602 / Num. obs: 139534 / % possible obs: 94.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1776 / Net I/av σ(I): 8.8 / Net I/σ(I): 1.89
Reflection shellResolution: 1.899→1.966 Å / Redundancy: 7 % / Rmerge(I) obs: 1.844 / Mean I/σ(I) obs: 1.14 / % possible all: 92.48

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Processing

Software
NameClassification
XDSdata scaling
Aimlessdata scaling
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4OGM

4ogm


Resolution: 1.899→38.58 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection
Rfree0.2326 -
Rwork0.1969 -
obs-139534
Refinement stepCycle: LAST / Resolution: 1.899→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11643 0 230 797 12670
LS refinement shellResolution: 1.899→1.966 Å / Rfactor Rfree: 0.3136 / Rfactor Rwork: 0.2887

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