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- PDB-4ogm: MBP-fusion protein of PilA1 residues 26-159 -

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Basic information

Entry
Database: PDB / ID: 4ogm
TitleMBP-fusion protein of PilA1 residues 26-159
ComponentsMaltose ABC transporter periplasmic protein, pilin protein chimera
KeywordsCELL ADHESION / Type IV pilin / fimbrial protein
Function / homology
Function and homology information


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 ...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 / periplasmic space / DNA damage response / membrane
Similarity search - Function
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 / : / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.234 Å
AuthorsPiepenbrink, K.H. / Sundberg, E.J.
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
DepositionJan 16, 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 18, 2015Group: Database references
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.pdbx_db_accession ..._struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer 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 / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: 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, pilin protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8012
Polymers56,4591
Non-polymers3421
Water5,657314
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.224, 74.710, 97.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose ABC transporter periplasmic protein, pilin protein chimera / MBP-PilA1


Mass: 56458.621 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: pMal E vector
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Clostridioides difficile (bacteria)
Gene: malE, HMPREF9530_03068, pulG, SAMEA3374973_02945 / Production host: Escherichia coli (E. coli)
References: UniProt: D8A942, UniProt: A0A1R2EY47, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS A CHIMERA COMPRISING ESCHERICHIA COLI MALTOSE ABC TRANSPORTER PERIPLASMIC PROTEIN (UNP ...PROTEIN IS A CHIMERA COMPRISING ESCHERICHIA COLI MALTOSE ABC TRANSPORTER PERIPLASMIC PROTEIN (UNP RESIDUES 27-387) AND CLOSTRIDIUM DIFFICILE PILIN PROTEIN (UNP RESIDUES 35-73) CONNECTED BY A AAAQTNAAA LINKER.

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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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2013
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.23→39.264 Å / Num. all: 23857 / Num. obs: 23856 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.212 / Net I/σ(I): 13.5
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
2.23-2.3111.11.920946188487.4
8.93-39.261259.7534744498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
PHASER2.5.5phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.234→39.264 Å / FOM work R set: 0.8064 / SU ML: 0.28 / σ(F): 1.89 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1999 8.4 %RANDOM
Rwork0.186 ---
all0.205 23852 --
obs0.1911 23804 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.39 Å2 / Biso mean: 24.45 Å2 / Biso min: 4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.234→39.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 23 314 4149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083916
X-RAY DIFFRACTIONf_angle_d1.1085322
X-RAY DIFFRACTIONf_chiral_restr0.041604
X-RAY DIFFRACTIONf_plane_restr0.006683
X-RAY DIFFRACTIONf_dihedral_angle_d12.7931426
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 (%)
2.234-2.28940.28931200.23481308142884
2.2894-2.35120.30181380.21451509164798
2.3512-2.42040.26891430.203715521695100
2.4204-2.49850.2641430.201515661709100
2.4985-2.58780.27791410.195515331674100
2.5878-2.69140.27631440.195115691713100
2.6914-2.81390.25921430.194615581701100
2.8139-2.96220.30971440.196315711715100
2.9622-3.14770.25461430.175315651708100
3.1477-3.39060.20931450.166315761721100
3.3906-3.73160.22291460.150615881734100
3.7316-4.2710.19371450.146315851730100
4.271-5.37880.19731490.162216221771100
5.3788-39.27020.28011550.23717031858100

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