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- PDB-4f8p: X-ray structure of PsaA from Yersinia pestis, in complex with gal... -

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Basic information

Entry
Database: PDB / ID: 4f8p
TitleX-ray structure of PsaA from Yersinia pestis, in complex with galactose
ComponentspH 6 antigen
KeywordsCELL ADHESION / Antigens / Bacterial Proteins / Fimbriae / Molecular Sequence Data / Protein Folding / Ig-fold
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
ACETATE ION / beta-D-galactopyranose / TERT-BUTYL FORMATE / pH 6 antigen
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 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 / 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pH 6 antigen
B: pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,25610
Polymers32,4982
Non-polymers7588
Water88349
1
A: pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7086
Polymers16,2491
Non-polymers4595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5474
Polymers16,2491
Non-polymers2983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.266, 59.266, 200.088
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 10 - 135 / Label seq-ID: 10 - 135

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

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


Mass: 16249.079 Da / Num. of mol.: 2
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: 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.: 2
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
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TBF / TERT-BUTYL FORMATE / TERTIARY BUTOXY CARBONYL / Tert-Butyl formate


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.4 M Sodium Formate, pH 4.5, 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: 4.7 % / Av σ(I) over netI: 11.76 / Number: 105458 / Rmerge(I) obs: 0.09 / Χ2: 1.18 / D res high: 2.07 Å / D res low: 50 Å / Num. obs: 22657 / % possible obs: 91.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.465097.610.0551.3028.6
3.544.4698.410.0791.0497.7
3.093.5497.510.1331.1276.2
2.813.0996.710.231.2094.9
2.612.8195.410.3751.3234
2.452.6194.110.4831.2173.5
2.332.459210.5221.1183.3
2.232.3389.910.5360.9762.6
2.142.2382.410.5290.9642.1
2.072.1472.810.5621.3571.7
ReflectionResolution: 2.05→50 Å / Num. obs: 22657 / % possible obs: 91.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Χ2: 1.176 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.141.70.56217791.357172.8
2.14-2.232.10.52920390.964182.4
2.23-2.332.60.53621940.976189.9
2.33-2.453.30.52222731.118192
2.45-2.613.50.48323371.217194.1
2.61-2.8140.37523461.323195.4
2.81-3.094.90.2323701.209196.7
3.09-3.546.20.13324251.127197.5
3.54-4.467.70.07924361.049198.4
4.46-508.60.05524581.302197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.587 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 1158 5.1 %RANDOM
Rwork0.2434 ---
obs0.2453 22654 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 124.53 Å2 / Biso mean: 50.2723 Å2 / Biso min: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 44 49 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212326
X-RAY DIFFRACTIONr_bond_other_d0.0670.0210
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9373151
X-RAY DIFFRACTIONr_angle_other_deg5.178319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5875281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18724.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.5115359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.701154
X-RAY DIFFRACTIONr_chiral_restr0.110.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211776
X-RAY DIFFRACTIONr_mcbond_it3.5531.51407
X-RAY DIFFRACTIONr_mcbond_other0.0331.53
X-RAY DIFFRACTIONr_mcangle_it5.46722260
X-RAY DIFFRACTIONr_scbond_it6.5223919
X-RAY DIFFRACTIONr_scangle_it9.1214.5891
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 979 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.480.5
MEDIUM THERMAL2.72
LS refinement shellResolution: 2.054→2.164 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.47 126 -
Rwork0.457 2460 -
all-2586 -
obs--72.72 %

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