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- PDB-4zyb: High resolution structure of M23 peptidase LytM with substrate an... -

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Basic information

Entry
Database: PDB / ID: 4zyb
TitleHigh resolution structure of M23 peptidase LytM with substrate analogue
ComponentsGlycyl-glycine endopeptidase LytM
KeywordsHYDROLASE / LYTM / LYSOSTAPHIN / PEPTIDOGLYCAN AMIDASE / PEPTIDASE / TETRAGLYCINE PHOSPHINATE / TRANSITION STATE ANALOGUE / COMPLEX
Function / homology
Function and homology information


lysostaphin / cobalt ion binding / peptide catabolic process / nickel cation binding / cell wall organization / metalloendopeptidase activity / metallopeptidase activity / manganese ion binding / proteolysis / zinc ion binding ...lysostaphin / cobalt ion binding / peptide catabolic process / nickel cation binding / cell wall organization / metalloendopeptidase activity / metallopeptidase activity / manganese ion binding / proteolysis / zinc ion binding / extracellular region / metal ion binding
Similarity search - Function
Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
tetraglycine phosphinate / DI(HYDROXYETHYL)ETHER / Unknown ligand / Glycyl-glycine endopeptidase LytM / Glycyl-glycine endopeptidase LytM
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGrabowska, M. / Jagielska, E. / Czapinska, H. / Bochtler, M. / Sabala, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
NCBiRPBS1/A8/8/2012 Poland
CitationJournal: Sci Rep / Year: 2015
Title: High resolution structure of an M23 peptidase with a substrate analogue.
Authors: Grabowska, M. / Jagielska, E. / Czapinska, H. / Bochtler, M. / Sabala, I.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs ..._reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rsym_value
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycyl-glycine endopeptidase LytM
B: Glycyl-glycine endopeptidase LytM
C: Glycyl-glycine endopeptidase LytM
D: Glycyl-glycine endopeptidase LytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,06729
Polymers58,2594
Non-polymers2,80825
Water15,565864
1
A: Glycyl-glycine endopeptidase LytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,63211
Polymers14,5651
Non-polymers1,06710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycyl-glycine endopeptidase LytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1557
Polymers14,5651
Non-polymers5906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycyl-glycine endopeptidase LytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2936
Polymers14,5651
Non-polymers7285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycyl-glycine endopeptidase LytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9875
Polymers14,5651
Non-polymers4224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.988, 101.563, 77.763
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycyl-glycine endopeptidase LytM / Autolysin LytM


Mass: 14564.811 Da / Num. of mol.: 4 / Fragment: unp residues 185-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: lytM, SAS0252 / Plasmid: PLASMID / Details (production host): PET15B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6GCJ6, UniProt: O33599*PLUS, lysostaphin

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Non-polymers , 9 types, 889 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 4 / Source method: obtained synthetically
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-4SQ / tetraglycine phosphinate


Mass: 281.203 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16N3O6P
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M HEPES-CsOH pH 7.5, 0.2 M calcium chloride and 25% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2013
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. obs: 87629 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rsym value: 0.112 / Net I/σ(I): 12
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.813 / Rsym value: 0.649 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B0P

2b0p


Resolution: 1.5→36.3 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.15 / Stereochemistry target values: ML
Details: The N-terminus of the truncated protein (absent in the full length native LytM) is disordered and has been built in only tentatively. The ligand could be reliably modelled in the C-terminal ...Details: The N-terminus of the truncated protein (absent in the full length native LytM) is disordered and has been built in only tentatively. The ligand could be reliably modelled in the C-terminal and phosphinate part, its N-terminus is most likely disordered, since none of its conformations was clearly prevailing in all four molecules in the asymmetric unit. There are numerous close contacts between solvent molecules in the structure which might either result from their static disorder, or poorly ordered PEG molecules, or low occupancy metal ions all of which have been modelled tentatively in a few cases. Alternatively they may result from crystal defects (crystallites of different symmetries forming the macroscopically observed crystal). The identity of a few ions is unsure - for the technical reasons the unsure Cl- ions were kept as Cl ions whereas the unsure Na ions have been submitted as UNL atoms. For a few serine residues we observe difference density close to the side chain oxygen atom.
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 4344 4.96 %Random selection
Rwork0.1497 ---
obs0.1514 87615 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 133 864 5068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064965
X-RAY DIFFRACTIONf_angle_d1.0676789
X-RAY DIFFRACTIONf_dihedral_angle_d15.0851864
X-RAY DIFFRACTIONf_chiral_restr0.08646
X-RAY DIFFRACTIONf_plane_restr0.004931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.4740.23782110.22073914X-RAY DIFFRACTION96
1.474-1.50080.23222260.19944173X-RAY DIFFRACTION100
1.5008-1.52970.22082420.18954164X-RAY DIFFRACTION100
1.5297-1.56090.22772380.1824116X-RAY DIFFRACTION100
1.5609-1.59490.2072410.17914162X-RAY DIFFRACTION100
1.5949-1.6320.21392000.17374162X-RAY DIFFRACTION100
1.632-1.67280.18741800.17094210X-RAY DIFFRACTION100
1.6728-1.7180.20652030.15974151X-RAY DIFFRACTION100
1.718-1.76850.19742440.15944205X-RAY DIFFRACTION100
1.7685-1.82560.20591940.15594109X-RAY DIFFRACTION100
1.8256-1.89090.19941930.14934258X-RAY DIFFRACTION100
1.8909-1.96660.20182120.15294132X-RAY DIFFRACTION100
1.9666-2.05610.17762400.14254146X-RAY DIFFRACTION100
2.0561-2.16450.1521940.13684201X-RAY DIFFRACTION100
2.1645-2.30.17262340.13934185X-RAY DIFFRACTION100
2.3-2.47760.15712090.14134187X-RAY DIFFRACTION100
2.4776-2.72690.20142380.14534147X-RAY DIFFRACTION100
2.7269-3.12120.17462390.14614155X-RAY DIFFRACTION100
3.1212-3.93170.19032270.12934209X-RAY DIFFRACTION100
3.9317-36.31230.14361790.13834285X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1161-0.2089-0.11050.39510.25970.30590.0235-0.00330.0636-0.05220.0055-0.0409-0.0569-0.02220.00030.05820.00240.00120.0602-0.00820.0671-1.750951.475874.2739
20.10940.04040.09150.22090.16860.24590.03250.00160.0286-0.0349-0.0233-0.01230.0224-0.007100.05720.00090.00260.0570.0060.054921.663777.619251.917
30.18510.2087-0.01610.27910.01130.30830.00720.0012-0.06090.0302-0.0029-0.05240.0253-0.0098-00.0576-0.0002-0.00430.0637-0.00680.068214.961450.498342.828
40.262-0.1099-0.08890.24210.10920.18910.01690.0339-0.05170.0432-0.0179-0.0097-0.0095-0.0148-0.00010.04710.00060.00080.04660.00040.03864.694924.423264.7425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or (chain K and resid 1) or (chain I and resid 1)
2X-RAY DIFFRACTION2chain B or (chain K and resid 2 ) or (chain I and resid 2)
3X-RAY DIFFRACTION3chain C or (chain K and resid 3) or (chain I and resid 3)
4X-RAY DIFFRACTION4chain D or (chain K and resid 4) or (chain I and resid 4 )

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