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- PDB-7sp2: Structure of PLS A-domain (residues 391-656; 513-518 deletion mut... -

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Basic information

Entry
Database: PDB / ID: 7sp2
TitleStructure of PLS A-domain (residues 391-656; 513-518 deletion mutant) from Staphylococcus aureus
ComponentsPlasmin Sensitive Protein Pls
KeywordsCELL ADHESION / L-type lectin
Function / homology
Function and homology information


extracellular region
Similarity search - Function
E domain / E domain / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsClark, L. / Whelan, F. / Atkin, K.E. / Brentnall, A.S. / Dodson, E.J. / Turkenburg, J.P. / Potts, J.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J005029/ United Kingdom
British Heart FoundationFS/12/36/29588 United Kingdom
British Heart FoundationPG/17/19/32862 United Kingdom
CitationJournal: Not Published
Title: Structure of PLS A-domain (residues 391-65) from Staphylococcus aureus
Authors: Clark, L. / Whelan, F. / Atkin, K.E. / Brentnall, A.S. / Dodson, E.J. / Turkenburg, J.P. / Potts, J.R.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.unpublished_flag
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmin Sensitive Protein Pls
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6442
Polymers28,6041
Non-polymers401
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Experimental SAXS scattering is consistent with the monomeric solution state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.210, 97.210, 97.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Plasmin Sensitive Protein Pls / 230 kDa cell-wall protein / Surface protein


Mass: 28604.240 Da / Num. of mol.: 1 / Fragment: A domain (UNP residues 391-656) / Mutation: del(513-518)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pls / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P80544
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v PEG3350, 0.1 M HEPES, pH 7.5, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.75→56.19 Å / Num. obs: 8201 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 74.57 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.056 / Net I/av σ(I): 10.6 / Net I/σ(I): 10
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 24.6 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 393 / CC1/2: 0.625 / Rpim(I) all: 0.614 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7sjk

7sjk


Resolution: 2.75→56.19 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.94 / SU B: 31.93 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 397 4.9 %RANDOM
Rwork0.2005 ---
obs0.2025 7783 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.14 Å2 / Biso mean: 80.187 Å2 / Biso min: 59.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.75→56.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 1 7 1980
Biso mean--79.17 70.31 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161825
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.6512722
X-RAY DIFFRACTIONr_angle_other_deg1.5511.5964187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.875257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30725.794107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53815321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.136154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
LS refinement shellResolution: 2.751→2.822 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 34 -
Rwork0.316 550 -
all-584 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -9.6755 Å / Origin y: -4.1316 Å / Origin z: 24.5892 Å
111213212223313233
T0.0366 Å2-0.0305 Å2-0.0226 Å2-0.1136 Å20.0099 Å2--0.0363 Å2
L2.5317 °20.5698 °20.0687 °2-2.79 °2-0.4272 °2--2.9453 °2
S-0.1935 Å °0.2913 Å °-0.0292 Å °-0.2355 Å °0.0784 Å °0.1271 Å °-0.0413 Å °-0.3412 Å °0.1151 Å °

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