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- PDB-2b13: Truncated S. aureus LytM, P41 crystal form -

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Basic information

Entry
Database: PDB / ID: 2b13
TitleTruncated S. aureus LytM, P41 crystal form
ComponentsGlycyl-glycine endopeptidase lytM
KeywordsHYDROLASE / LytM / lysostaphin / peptidoglycan amidase / peptidase
Function / homology
Function and homology information


lysostaphin / cobalt ion binding / peptide catabolic process / nickel cation binding / cell wall organization / metalloendopeptidase activity / manganese ion binding / proteolysis / zinc ion binding / extracellular region
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
L(+)-TARTARIC ACID / Glycyl-glycine endopeptidase LytM
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFirczuk, M. / Mucha, A. / Bochtler, M.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of active LytM.
Authors: Firczuk, M. / Mucha, A. / Bochtler, M.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Latent LytM at 1.3A resolution.
Authors: Odintsov, S.G. / Sabala, I. / Marcyjaniak, M. / Bochtler, M.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 17, 2017Group: Non-polymer description
Revision 1.4Aug 23, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Glycyl-glycine endopeptidase lytM
B: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5616
Polymers29,1302
Non-polymers4314
Water6,161342
1
A: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7803
Polymers14,5651
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7803
Polymers14,5651
Non-polymers2152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.962, 65.962, 62.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 14564.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lytM / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O33599, lysostaphin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 % PEG 8000, 0.2 M L(+)-tartrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2005 / Details: Osmic Max-Flux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→14.8 Å / Num. all: 38546 / Num. obs: 38546 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 25.8
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 10 / Num. unique all: 1803 / Rsym value: 0.152 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QWY

1qwy


Resolution: 1.55→14.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.83 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20054 1940 5 %RANDOM
Rwork0.17157 ---
all0.17303 36606 --
obs0.17303 36606 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.55→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 22 342 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212078
X-RAY DIFFRACTIONr_bond_other_d00.021652
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9052826
X-RAY DIFFRACTIONr_angle_other_deg3.99433872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022422
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02426
X-RAY DIFFRACTIONr_nbd_refined0.2220.2384
X-RAY DIFFRACTIONr_nbd_other0.2980.21833
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1150.21010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0360.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.871.51284
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51122036
X-RAY DIFFRACTIONr_scbond_it2.4173794
X-RAY DIFFRACTIONr_scangle_it3.7794.5790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 143
Rwork0.251 2579
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)
10.85140.11650.11920.4966-0.07720.38020.00350.02280.0382-0.03420.0007-0.01640.021-0.0362-0.00420.0125-0.00550.00440.03960.00440.0026-8.35426.074.016
20.2995-0.13860.03490.46380.06080.36480.0152-0.0217-0.01340.00410.0009-0.00410.0055-0.0139-0.01610.02820.0019-0.00550.03120.00390.00920.9718.39615.934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA185 - 3153 - 133
2X-RAY DIFFRACTION2BB185 - 3153 - 133

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