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- PDB-4pe2: MBP PilA1 CD160 -

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Basic information

Entry
Database: PDB / ID: 4pe2
TitleMBP PilA1 CD160
ComponentsMaltose ABC transporter periplasmic protein,Prepilin-type N-terminal cleavage/methylation domain protein
KeywordsCELL ADHESION / T4P / Pilin
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 binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport ...protein secretion by the type II secretion system / type II protein secretion system complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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-maltose / MALONATE ION / Maltose/maltodextrin-binding periplasmic protein / Prepilin-type N-terminal cleavage/methylation domain protein / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Clostridium difficile CD160 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.724 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)1 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
DepositionApr 22, 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 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / refine_hist / 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_atom_id / _atom_site.label_comp_id / _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.type / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Maltose ABC transporter periplasmic protein,Prepilin-type N-terminal cleavage/methylation domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9223
Polymers56,4781
Non-polymers4442
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint4 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.484, 70.468, 117.153
Angle α, β, γ (deg.)90.000, 90.240, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-602-

MLI

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Components

#1: Protein Maltose ABC transporter periplasmic protein,Prepilin-type N-terminal cleavage/methylation domain protein / PilA1


Mass: 56477.602 Da / Num. of mol.: 1 / Fragment: MBP residues 27-392, PilA1 residues 35-169 / Mutation: G104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Clostridium difficile CD160 (bacteria)
Gene: malE, BN896_3748, QEW_4140 / Strain: CD160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: U6NJU2, UniProt: T3D4G1, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.4 Å3/Da / Density % sol: 48.76 % / Description: Plate-like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.72→36.6 Å / Num. obs: 51443 / % possible obs: 95.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.052 / Net I/σ(I): 8.3 / Num. measured all: 334150
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.72-1.7641.5640.7692317190.82958.1
8.96-36.66.40.07221.925223930.0397

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å36.6 Å
Translation3 Å36.6 Å

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Processing

Software
NameVersionClassification
XDS0.1.26data reduction
SCALAdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.724→36.595 Å / FOM work R set: 0.8076 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 2000 3.91 %Random selection
Rwork0.1968 49180 --
obs0.1978 51180 95.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.2 Å2 / Biso mean: 33.3 Å2 / Biso min: 13.67 Å2
Refinement stepCycle: final / Resolution: 1.724→36.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 30 364 4181
Biso mean--25.29 38.62 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083897
X-RAY DIFFRACTIONf_angle_d1.0735296
X-RAY DIFFRACTIONf_chiral_restr0.044602
X-RAY DIFFRACTIONf_plane_restr0.005679
X-RAY DIFFRACTIONf_dihedral_angle_d13.0031426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.724-1.76690.3842920.35162207229960
1.7669-1.81470.40091400.3363471361194
1.8147-1.86810.38851520.31593623377599
1.8681-1.92830.32421550.27963630378599
1.9283-1.99730.34131440.25773593373798
1.9973-2.07720.2591400.23193589372997
2.0772-2.17180.24281480.21053597374599
2.1718-2.28620.24621470.21113641378899
2.2862-2.42940.25891480.20123612376098
2.4294-2.6170.21491440.19983587373198
2.617-2.88020.22791480.20023651379999
2.8802-3.29680.2071430.19013612375598
3.2968-4.15270.16581510.16343692384399
4.1527-36.60350.18731480.16593675382398

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