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- PDB-7sjk: Structure of PLS A-domain (residues 391-656) from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 7sjk
TitleStructure of PLS A-domain (residues 391-656) from Staphylococcus aureus
ComponentsPls Plasmin sensitive surface protein
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 subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.208 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: J.Biol.Chem. / Year: 2023
Title: Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface.
Authors: Clark, L.C. / Atkin, K.E. / Whelan, F. / Brentnall, A.S. / Harris, G. / Towell, A.M. / Turkenburg, J.P. / Liu, Y. / Feizi, T. / Griffiths, S.C. / Geoghegan, J.A. / Potts, J.R.
History
DepositionOct 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
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: Pls Plasmin sensitive surface protein
B: Pls Plasmin sensitive surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5744
Polymers58,4942
Non-polymers802
Water13,259736
1
A: Pls Plasmin sensitive surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2872
Polymers29,2471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pls Plasmin sensitive surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2872
Polymers29,2471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.150, 66.689, 71.506
Angle α, β, γ (deg.)90.000, 110.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 393 - 653 / Label seq-ID: 7 - 267

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

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Components

#1: Protein Pls Plasmin sensitive surface protein / 230 kDa cell-wall protein / Plasmin-sensitive surface protein


Mass: 29247.025 Da / Num. of mol.: 2 / Fragment: A domain (UNP residues 391-656)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (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.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.208→67.17 Å / Num. obs: 139773 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 7.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.093 / Rrim(I) all: 0.137 / Χ2: 0.91 / Net I/σ(I): 5.8
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6855 / CC1/2: 0.391 / Rpim(I) all: 0.785 / Χ2: 0.96 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4CCI

4cci
PDB Unreleased entry


Resolution: 1.208→67.06 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.936 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1577 7281 5.2 %RANDOM
Rwork0.12 ---
obs0.122 132407 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.61 Å2 / Biso mean: 14.758 Å2 / Biso min: 6.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20.3 Å2
2--1.52 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.208→67.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 2 748 4778
Biso mean--9.16 28.34 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0134641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164266
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.6526334
X-RAY DIFFRACTIONr_angle_other_deg1.5731.6019864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50326.125240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68615792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.258158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025761
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021131
X-RAY DIFFRACTIONr_rigid_bond_restr5.47838905
Refine LS restraints NCS

Ens-ID: 1 / Number: 8685 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.208→1.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 536 -
Rwork0.223 9271 -
all-9807 -
obs--95.15 %

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