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- PDB-4f8l: X-ray structure of PsaA from Yersinia pestis, in complex with gal... -

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Basic information

Entry
Database: PDB / ID: 4f8l
TitleX-ray structure of PsaA from Yersinia pestis, in complex with galactose and AEBSF
ComponentspH 6 antigen
KeywordsCELL ADHESION/inhibitor / Antigens / Bacterial Proteins / Fimbriae / Molecular Sequence Data / Protein Folding / All Beta-strand / Ig-fold / Adhesion / 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
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / BROMIDE ION / GUANIDINE / beta-D-galactopyranose / GLYCINE / MALONATE ION / pH 6 antigen
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 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 / Item: _software.classification
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 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

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Assembly

Deposited unit
A: pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,74542
Polymers16,2491
Non-polymers3,49641
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.108, 54.164, 101.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-214-

BR

21A-324-

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, y2882, YPO1303, YP_1289 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31522
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 186 molecules

#3: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#5: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF / AEBSF


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#6: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 298 K / pH: 4.2
Details: 1.5 M ammonium sulphate, 0.17 M 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: 0.9
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: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / % possible obs: 96.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.538 / % possible all: 90.7

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVEphasing
DMphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→27.08 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.3 / σ(F): 1.35 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 1178 5.12 %
Rwork0.139 --
obs0.141 23029 95.9 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.69 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.6641 Å20 Å2-0 Å2
2--6.5375 Å2-0 Å2
3----4.8734 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 76 146 1295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131164
X-RAY DIFFRACTIONf_angle_d1.3931578
X-RAY DIFFRACTIONf_dihedral_angle_d13.775414
X-RAY DIFFRACTIONf_chiral_restr0.317170
X-RAY DIFFRACTIONf_plane_restr0.007202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56680.28251150.20112247X-RAY DIFFRACTION80
1.5668-1.64940.21821430.18362598X-RAY DIFFRACTION93
1.6494-1.75280.20651710.15222740X-RAY DIFFRACTION98
1.7528-1.88810.20021470.12592754X-RAY DIFFRACTION98
1.8881-2.0780.15091440.10912793X-RAY DIFFRACTION99
2.078-2.37860.15071490.11562814X-RAY DIFFRACTION99
2.3786-2.99610.16861450.13252878X-RAY DIFFRACTION99
2.9961-27.08640.18361640.1493027X-RAY DIFFRACTION100

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