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- PDB-4ivv: Catalytic amidase domain of the major autolysin LytA from Strepto... -

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Basic information

Entry
Database: PDB / ID: 4ivv
TitleCatalytic amidase domain of the major autolysin LytA from Streptococcus pneumaniae
ComponentsAutolysin
KeywordsHYDROLASE / amidase-2 / LytA / peptidoglycan cleavage / autolysin
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsSandalova, T. / Achour, A.
CitationJournal: MBio / Year: 2014
Title: Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
Authors: Mellroth, P. / Sandalova, T. / Kikhney, A. / Vilaplana, F. / Hesek, D. / Lee, M. / Mobashery, S. / Normark, S. / Svergun, D. / Henriques-Normark, B. / Achour, A.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3943
Polymers21,2661
Non-polymers1272
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.440, 50.440, 72.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Autolysin / / Cell wall hydrolase / Mucopeptide aminohydrolase / Murein hydrolase / N-acetylmuramoyl-L-alanine amidase


Mass: 21266.330 Da / Num. of mol.: 1 / Fragment: N-LytA, UNP residues 1-181 / Mutation: C60A, C136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: strain ATCC BAA-334 / TIGR4 / Gene: lytA, SP_1937 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 6000 12%, 0.1M TrisHCl, LiCl 0.8M, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.05→43.7 Å / Num. all: 95581 / Num. obs: 95581 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.3
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.7 / Num. unique all: 14111 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXSphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.05→17.46 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.642 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15703 4816 5 %RANDOM
Rwork0.14131 ---
all0.1421 91206 --
obs0.1421 91206 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.847 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.05→17.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 5 255 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211478
X-RAY DIFFRACTIONr_bond_other_d0.0010.02964
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9212023
X-RAY DIFFRACTIONr_angle_other_deg0.84732360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2082580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.51415230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.671156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
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_it0.8121.5893
X-RAY DIFFRACTIONr_mcbond_other0.1921.5363
X-RAY DIFFRACTIONr_mcangle_it1.36721446
X-RAY DIFFRACTIONr_scbond_it1.9653585
X-RAY DIFFRACTIONr_scangle_it3.0174.5571
X-RAY DIFFRACTIONr_rigid_bond_restr0.66432442
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 343 -
Rwork0.284 6830 -
obs--99.83 %

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