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- PDB-4pi9: Crystal structure of S. Aureus Autolysin E in complex with murope... -

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Basic information

Entry
Database: PDB / ID: 4pi9
TitleCrystal structure of S. Aureus Autolysin E in complex with muropeptide NAM-L-ALA-D-iGLU
ComponentsAutolysin E
KeywordsHYDROLASE / autolysin / glycosidase / peptidoglycan / muropeptide
Function / homologyLysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / amidase activity / membrane / Chem-3LT / Autolysin E (1e-98,63%,84%,258-258)
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsMihelic, M. / Renko, M. / 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 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)27,09712
Polymers26,0681
Non-polymers1,02911
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-89 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.626, 69.312, 73.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV2307 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3JT72
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-3LT / (4R)-4-[[(2S)-2-[[(2R)-2-[(2R,3S,4R,5R,6R)-5-acetamido-2-(hydroxymethyl)-3,6-bis(oxidanyl)oxan-4-yl]oxypropanoyl]amino]propanoyl]amino]-5-azanyl-5-oxidanylidene-pentanoic acid


Mass: 492.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32N4O11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2014
RadiationMonochromator: Si111-DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.48→38.75 Å / Num. obs: 39606 / % possible obs: 99.55 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 27.477 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Χ2: 1.234 / Net I/σ(I): 20.16 / Num. measured all: 251926
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.48-1.536.50.7460.74622.074045112207118690.73496.26
1.57-1.670.8820.3762.743777711415113990.4599.9
1.67-1.810.9510.2224.733628610711106860.26399.8
1.81-1.980.9850.1198.9534350985298350.14199.8
1.98-2.210.9940.06416.0728735885487660.07799
2.21-2.550.9970.04525.0227066782777340.05398.8
2.55-3.130.9980.03432.2920869660864380.04197.4
3.13-4.410.9990.02444.4316999514250320.02997.9
4.410.9990.0246.759393284128030.02498.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.48→38.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.63 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20936 1981 5 %RANDOM
Rwork0.17708 ---
obs0.17873 37625 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2---0.85 Å20 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.48→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 56 237 2081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021895
X-RAY DIFFRACTIONr_bond_other_d0.0030.021791
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9682549
X-RAY DIFFRACTIONr_angle_other_deg1.0023.0084137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57425.31396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35915355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3592.614895
X-RAY DIFFRACTIONr_mcbond_other2.3312.608893
X-RAY DIFFRACTIONr_mcangle_it3.6293.9021115
X-RAY DIFFRACTIONr_mcangle_other3.6243.9021115
X-RAY DIFFRACTIONr_scbond_it3.1892.9211000
X-RAY DIFFRACTIONr_scbond_other3.1872.921001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.984.2251432
X-RAY DIFFRACTIONr_long_range_B_refined7.7422.022405
X-RAY DIFFRACTIONr_long_range_B_other7.73922.0212406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 137 -
Rwork0.301 2594 -
obs--94.96 %

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