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- PDB-4pi8: Crystal structure of catalytic mutant E138A of S. Aureus Autolysi... -

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Basic information

Entry
Database: PDB / ID: 4pi8
TitleCrystal structure of catalytic mutant E138A of S. Aureus Autolysin E in complex with disaccharide NAG-NAM
ComponentsAutolysin E
KeywordsHYDROLASE / autolysin / peptidoglycan / glycosidase
Function / homology
Function and homology information


amidase activity / bacterial-type flagellum-dependent cell motility / membrane => GO:0016020 / extracellular region / membrane
Similarity search - Function
Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
Similarity search - Domain/homology
Autolysin E (1e-98,63%,84%,258-258) / Autolysin E (1e-98,63%,84%,258-258)
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsMihelic, M. / Renko, M. / Jakas, A. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autolysin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,09917
Polymers26,0101
Non-polymers1,08916
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-135 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.011, 69.720, 73.540
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: 26010.244 Da / Num. of mol.: 1 / Fragment: UNP residues 35-258 / Mutation: E138A
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): BL21DE3 / References: UniProt: Q99RW6, UniProt: A0A0H3JT72*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 46.39 %
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: PSI 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
ReflectionNumber: 312334 / Rmerge(I) obs: 0.032 / Χ2: 1.04 / D res high: 1.39 Å / Num. obs: 91609 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
2.944.15620910.019
2.42.94798810.024
2.082.4954410.031
1.862.081081810.049
1.71.861191210.091
1.581.71301210.156
1.471.581393210.27
1.391.471476810.477
ReflectionResolution: 1.39→38.4 Å / Num. obs: 48332 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 23.374 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.0344 / Rrim(I) all: 0.038 / Χ2: 1.042 / Net I/σ(I): 26.9 / Num. measured all: 312334
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
1.39-1.446.50.8390.592735034414864147680.56799.69
1.47-1.580.9320.274.184568513995139320.32299.5
1.58-1.70.9760.1567.284539313028130120.18599.9
1.7-1.860.9910.09111.573976211955119120.10899.6
1.86-2.080.9970.04921.023794710852108180.05899.7
2.08-2.40.9990.03132.3832410959495440.03799.5
2.4-2.940.9990.02443.6628367803479880.02999.4
2.94-4.150.9990.01955.7720706627162090.02299
4.150.9990.01762.4411720345234260.0299.2

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.39→38.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1771 / WRfactor Rwork: 0.1517 / FOM work R set: 0.8923 / SU B: 0.877 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0515 / SU Rfree: 0.0536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 2417 5 %RANDOM
Rwork0.152 45915 --
obs0.1532 48332 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.69 Å2 / Biso mean: 22.531 Å2 / Biso min: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å2-0 Å2
2---0.83 Å20 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.39→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 53 256 2098
Biso mean--21.38 34.39 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191915
X-RAY DIFFRACTIONr_bond_other_d0.0010.021818
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9682578
X-RAY DIFFRACTIONr_angle_other_deg0.92334207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0945232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44425.5198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37615368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.387158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_mcbond_it1.9811.919898
X-RAY DIFFRACTIONr_mcbond_other1.9541.917897
X-RAY DIFFRACTIONr_mcangle_it3.0792.8681122
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 176 -
Rwork0.247 3340 -
all-3516 -
obs--99.58 %

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