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- PDB-4pia: Crystal structure of S. Aureus Autolysin E -

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Basic information

Entry
Database: PDB / ID: 4pia
TitleCrystal structure of S. Aureus Autolysin E
ComponentsAutolysin E
KeywordsHYDROLASE / autolysin / glycosidase / peptidoglycan
Function / homologyLysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / amidase activity / membrane => GO:0016020 / extracellular region / Autolysin E (1e-98,63%,84%,258-258) / Autolysin E (1e-98,63%,84%,258-258)
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.466 Å
AuthorsMihelic, M. / Renko, M. / Dobersek, A. / Bedrac, L. / Turk, D.
CitationJournal: Iucrj / Year: 2017
Title: The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers
Authors: Mihelic, M. / Vlahovicek-Kahlina, K. / Renko, M. / Mesnage, S. / Dobersek, A. / Taler-Vercic, A. / Jakas, A. / Turk, D.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Autolysin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38710
Polymers26,0681
Non-polymers3199
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-71 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.599, 69.927, 73.268
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 Autolysin E


Mass: 26068.279 Da / Num. of mol.: 1 / Fragment: UNP residues 35-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV2307 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99RW6, UniProt: A0A0H3JT72*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M (NH4)2SO4, 2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→23 Å / Num. obs: 41563 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.043 / Χ2: 0.655 / Net I/av σ(I): 33.475 / Net I/σ(I): 39.2 / Num. measured all: 229537
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.46-1.4940.29112640.80295.97
1.49-1.515.30.25920800.60799.4
1.51-1.545.50.21420830.56100
1.54-1.575.50.18520770.51899.8
1.57-1.615.50.1621050.48899.8
1.61-1.645.50.13920860.481100
1.64-1.695.50.11820950.50899.9
1.69-1.735.50.10920860.542100
1.73-1.785.60.09421040.51199.9
1.78-1.845.60.0821030.526100
1.84-1.915.60.06820900.557100
1.91-1.985.60.05821170.608100
1.98-2.075.70.04720930.609100
2.07-2.185.70.04221230.639100
2.18-2.325.70.03821300.68100
2.32-2.55.70.03621400.708100
2.5-2.755.70.03321410.731100
2.75-3.145.70.03121450.847100
3.14-3.965.60.02821951.031100
3.96-235.30.03123061.171100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
RefinementResolution: 1.466→23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1694 / WRfactor Rwork: 0.1445 / FOM work R set: 0.9053 / SU B: 0.862 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0583 / SU Rfree: 0.0594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 2090 5 %RANDOM
Rwork0.1492 39382 --
obs0.1503 41472 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 15.919 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.466→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 9 258 2076
Biso mean--22.08 28.17 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021883
X-RAY DIFFRACTIONr_bond_other_d0.0010.021789
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9472533
X-RAY DIFFRACTIONr_angle_other_deg0.88134140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1435237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29425.61298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.097158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_mcbond_it1.5311.297912
X-RAY DIFFRACTIONr_mcbond_other1.5081.295911
X-RAY DIFFRACTIONr_mcangle_it2.3541.9371140
LS refinement shellResolution: 1.466→1.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 152 -
Rwork0.195 2730 -
all-2882 -
obs--94.65 %

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