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- PDB-2b0p: truncated S. aureus LytM, P212121 crystal form -

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Basic information

Entry
Database: PDB / ID: 2b0p
Titletruncated S. aureus LytM, P212121 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 / extracellular region / zinc 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
ACETATE ION / CACODYLATE ION / Glycyl-glycine endopeptidase LytM
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 14, 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 1.3Aug 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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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)29,7129
Polymers29,1302
Non-polymers5827
Water6,936385
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A: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8855
Polymers14,5651
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8264
Polymers14,5651
Non-polymers2613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.093, 78.261, 102.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 0.1 M sodium acetate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 42130 / Num. obs: 42130 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6060 / Rsym value: 0.256 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QWY

1qwy


Resolution: 1.5→19.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.205 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22239 2082 5 %RANDOM
Rwork0.18039 ---
all0.184 42059 --
obs0.18241 39977 99.95 %-
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: 10.184 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2---0.46 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 24 385 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212051
X-RAY DIFFRACTIONr_bond_other_d00.021653
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9092787
X-RAY DIFFRACTIONr_angle_other_deg4.00333858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325256
X-RAY DIFFRACTIONr_chiral_restr0.1150.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022396
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02426
X-RAY DIFFRACTIONr_nbd_refined0.1930.2365
X-RAY DIFFRACTIONr_nbd_other0.2960.21856
X-RAY DIFFRACTIONr_nbtor_other0.1140.2997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2260
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.232
X-RAY DIFFRACTIONr_mcbond_it1.0751.51275
X-RAY DIFFRACTIONr_mcangle_it1.66822014
X-RAY DIFFRACTIONr_scbond_it2.6163776
X-RAY DIFFRACTIONr_scangle_it3.8844.5773
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 170
Rwork0.268 2849
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)
10.24030.08540.17111.03360.43671.23320.0103-0.04770.01740.0006-0.0058-0.0420.0404-0.0278-0.00450.00020.0046-0.00370.1962-0.00720.18067.278-3.780.321
20.43820.0199-0.02220.80720.01790.71950.01070.0297-0.03260.01680.0011-0.00220.0082-0.0135-0.01190.02-0.00730.0020.18180.00150.18880.703-13.17-26.479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA188 - 3166 - 134
2X-RAY DIFFRACTION2BB188 - 3166 - 134

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