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- PDB-7sie: Structure of AAP A-domain (residues 351-605) from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 7sie
TitleStructure of AAP A-domain (residues 351-605) from Staphylococcus epidermidis
ComponentsAccumulation associated protein
KeywordsCELL ADHESION / L-type lectin / Staphylococcus epidermidis
Function / homology
Function and homology information


E domain / E domain / Bacterial lectin / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif ...E domain / E domain / Bacterial lectin / 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
Accumulation associated protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsAtkin, K.E. / Brentnall, A.S. / Dodson, E.J. / Whelan, F. / Clark, L. / 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 13, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionOct 19, 2022ID: 4CCI
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5013
Polymers29,4261
Non-polymers762
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-15 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.853, 68.693, 109.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Accumulation associated protein


Mass: 29425.748 Da / Num. of mol.: 1 / Fragment: A domain (UNP residues 338-608)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 35984 / RP62A) (bacteria)
Strain: ATCC 35984 / RP62A / Gene: aap, SERP2398 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HKE8
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M LiCl, 10% PEG6000, 0.1 M sodium acetate, pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013 / Details: MIRROR PAIR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.3→58.145 Å / Num. obs: 66898 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Num. unique obs: 3479 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→16.53 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.769 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1243 3351 5 %RANDOM
Rwork0.0998 ---
obs0.1011 63480 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.03 Å2 / Biso mean: 10.078 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0 Å2
2---0.11 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.3→16.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 2 385 2345
Biso mean--6.36 24.03 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0122198
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151922
X-RAY DIFFRACTIONr_angle_refined_deg2.071.6623010
X-RAY DIFFRACTIONr_angle_other_deg1.6241.5984446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84224.146123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2915337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8031510
X-RAY DIFFRACTIONr_chiral_restr0.1190.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022747
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02565
X-RAY DIFFRACTIONr_rigid_bond_restr3.56734120
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.123 234 -
Rwork0.073 4589 -
all-4823 -
obs--98.87 %

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