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- PDB-6fxo: Crystal structure of Major Bifunctional Autolysin -

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Basic information

Entry
Database: PDB / ID: 6fxo
TitleCrystal structure of Major Bifunctional Autolysin
ComponentsBifunctional autolysin
KeywordsHYDROLASE / peptidoglycan hydrolase / GH73 / glycoside hydrolase family 73 / autolysin
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / N-acetylmuramoyl-L-alanine amidase / amidase activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Ami_2 / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
Bifunctional autolysin
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPintar, S. / Turk, D.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0048 Slovenia
CitationJournal: Commun Biol / Year: 2020
Title: Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis.
Authors: Pintar, S. / Borisek, J. / Usenik, A. / Perdih, A. / Turk, D.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / computing / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.number_reflns_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.percent_possible_all / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Description: Polymer geometry
Details: Dear Deposit-Help, We updated our 6FXO deposit on the initiative of a reviewer. Due to low intensity of data, we decided to truncate resolution to 2.5A. Best, Sara and Dusan
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3184
Polymers27,2121
Non-polymers1063
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-23 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.168, 110.168, 92.39
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Bifunctional autolysin


Mass: 27211.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: atl, nag, SAV1052 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q931U5, N-acetylmuramoyl-L-alanine amidase, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.28→42.39 Å / Num. obs: 15697 / % possible obs: 99.8 % / Redundancy: 21.1 % / CC1/2: 1 / Rrim(I) all: 0.091 / Net I/σ(I): 25.31
Reflection shellResolution: 2.28→2.41 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2453 / CC1/2: 0.631 / Rrim(I) all: 1.626 / % possible all: 99.3

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Processing

Software
NameClassification
MAINrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SagB

Resolution: 2.5→35.4 Å / Cor.coef. Fo:Fc: 0.8908 / Cor.coef. Fo:Fc free: 0.8681 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.1 / Details: Instead of Rfree, Rkick was used
RfactorNum. reflection% reflectionSelection details
Rfree0.33 11943 100 %NONE
Rwork0.2948 ---
all0.2948 ---
obs0.2948 11943 100 %-
Solvent computationBsol: 37.98 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 0 Å2 / Biso mean: 0 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.033 Å20 Å20 Å2
2---0.033 Å20 Å2
3---0.067 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 3 54 1884
LS refinement shellResolution: 2.5→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3526 578 100 %
Rwork0.2963 578 -
all-578 -
obs-578 1 %

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