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- PDB-5ln4: Crystal structure of self-complemented PsaA, the major subunit of... -

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Basic information

Entry
Database: PDB / ID: 5ln4
TitleCrystal structure of self-complemented PsaA, the major subunit of pH 6 antigen from Yersinia pests, in complex with choline
ComponentspH 6 antigen,pH 6 antigen
KeywordsCELL ADHESION / Ig-like fold / beta sandwich / donor-strand complementation
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
CHOLINE ION / pH 6 antigen
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsPakharukova, N.A. / Roy, S. / Rahman, M.M. / Tuitilla, M. / Zavialov, A.V.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland140959 Finland
Academy of Finland273075 Finland
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structural basis for Myf and Psa fimbriae-mediated tropism of pathogenic strains of Yersinia for host tissues.
Authors: Pakharukova, N. / Roy, S. / Tuittila, M. / Rahman, M.M. / Paavilainen, S. / Ingars, A.K. / Skaldin, M. / Lamminmaki, U. / Hard, T. / Teneberg, S. / Zavialov, A.V.
History
DepositionAug 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _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,pH 6 antigen
B: pH 6 antigen,pH 6 antigen
C: pH 6 antigen,pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5556
Polymers44,2423
Non-polymers3133
Water3,333185
1
A: pH 6 antigen,pH 6 antigen


Theoretical massNumber of molelcules
Total (without water)14,7471
Polymers14,7471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pH 6 antigen,pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9563
Polymers14,7471
Non-polymers2082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: pH 6 antigen,pH 6 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8522
Polymers14,7471
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.542, 44.625, 99.441
Angle α, β, γ (deg.)90.000, 120.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14747.446 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: psaA, YPO1303, y2882, YP_1289 / Plasmid: pET101D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P31522
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.56 Å3/Da / Density % sol: 65.45 % / Mosaicity: 0.28 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M imidazole, 0.2 M zinc acetate and 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.36→49.4 Å / Num. obs: 25917 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rsym value: 0.082 / Net I/av σ(I): 8.857 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.36-2.443.50.631.2199.6
2.44-2.543.50.5371.4199.5
2.54-2.643.30.42199.3
2.64-2.763.60.2862.7199.8
2.76-2.893.60.2043.8199.8
2.89-3.053.50.1535.1199.6
3.05-3.233.30.1067.3199.2
3.23-3.453.60.0849.1199.8
3.45-3.733.50.06112.3199.8
3.73-4.093.40.05114.6199.1
4.09-4.573.40.03918.1199.7
4.57-5.283.50.03719.1199.5
5.28-6.463.20.04117.5199.6
6.46-9.143.40.03618.8199.5
9.14-49.39730.02622.8198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LND

5lnd


Resolution: 2.36→49.397 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.276 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.237 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1322 5.1 %RANDOM
Rwork0.2294 ---
obs0.2314 24595 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.92 Å2 / Biso mean: 44.315 Å2 / Biso min: 8.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å21.48 Å2
2---2.36 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 2.36→49.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 21 185 3322
Biso mean--45.18 46.2 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023218
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.9444373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1125396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84424.894141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43915506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.292156
X-RAY DIFFRACTIONr_chiral_restr0.1290.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212460
X-RAY DIFFRACTIONr_mcbond_it3.6714.3291593
X-RAY DIFFRACTIONr_mcangle_it5.4896.4811986
X-RAY DIFFRACTIONr_scbond_it4.6674.4651623
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 90 -
Rwork0.309 1787 -
all-1877 -
obs--99.58 %

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