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- PDB-4f8o: X-ray structure of PsaA from Yersinia pestis, in complex with lac... -

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Basic information

Entry
Database: PDB / ID: 4f8o
TitleX-ray structure of PsaA from Yersinia pestis, in complex with lactose and AEBSF
ComponentspH 6 antigen
KeywordsCELL ADHESION/inhibitor / Antigens / Bacterial Proteins / Fimbriae / Molecular Sequence Data / Protein Folding / Ig-fold / CELL ADHESION-inhibitor complex
Function / homology
Function and homology information


Immunoglobulin-like - #3590 / : / : / Ph 6 antigen / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-lactose / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / GUANIDINE / pH 6 antigen
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBao, R. / Esser, L. / Xia, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for the specific recognition of dual receptors by the homopolymeric pH 6 antigen (Psa) fimbriae of Yersinia pestis.
Authors: Bao, R. / Nair, M.K. / Tang, W.K. / Esser, L. / Sadhukhan, A. / Holland, R.L. / Xia, D. / Schifferli, D.M.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / struct_conn / struct_ref_seq_dif / 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 / _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 / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9486
Polymers16,2491
Non-polymers6995
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.264, 55.694, 103.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-374-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein pH 6 antigen / Adhesin / Antigen 4


Mass: 16249.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: psaA, YPO1303, y2882, YP_1289 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31522
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 105 molecules

#3: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: ammonium sulphate, Guanidine HCl, pH 4.2, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 2.6 % / Av σ(I) over netI: 6.29 / Number: 41798 / Rmerge(I) obs: 0.115 / Χ2: 0.97 / D res high: 1.61 Å / D res low: 50 Å / Num. obs: 16080 / % possible obs: 92.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.475095.710.0540.9533.2
2.753.4796.110.0850.9343
2.42.7596.410.1511.013
2.192.495.910.2121.0412.9
2.032.1993.510.271.0422.8
1.912.0393.910.341.0752.5
1.811.9191.610.3941.0922.3
1.731.8189.510.4321.0022.1
1.671.7386.410.4530.7252
1.611.6784.710.4670.6161.9
ReflectionResolution: 1.61→50 Å / Num. obs: 16080 / % possible obs: 92.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.115 / Χ2: 0.974 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.61-1.671.90.46714650.616184.7
1.67-1.7320.45314320.725186.4
1.73-1.812.10.43215271.002189.5
1.81-1.912.30.39415771.092191.6
1.91-2.032.50.3415891.075193.9
2.03-2.192.80.2716071.042193.5
2.19-2.42.90.21216641.041195.9
2.4-2.7530.15117031.01196.4
2.75-3.4730.08516940.934196.1
3.47-503.20.05418220.953195.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHENIX1.7.2_869refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15.387 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.69 / σ(F): 1.46 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2863 598 4.98 %
Rwork0.2411 --
obs0.2433 12006 94.99 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.659 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 69.49 Å2 / Biso mean: 27.0788 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.5274 Å20 Å20 Å2
2--0.292 Å20 Å2
3---0.2354 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 44 101 1214

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