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- PDB-2b44: Truncated S. aureus LytM, P 32 2 1 crystal form -

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Basic information

Entry
Database: PDB / ID: 2b44
TitleTruncated S. aureus LytM, P 32 2 1 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
PHOSPHATE ION / Glycyl-glycine endopeptidase LytM
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsFirczuk, M. / Mucha, A. / Bochtler, M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of active LytM.
Authors: Firczuk, M. / Mucha, A. / Bochtler, M.
History
DepositionSep 22, 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: 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 / 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_alt_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_alt_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.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_label_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: Glycyl-glycine endopeptidase lytM
B: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2837
Polymers28,8672
Non-polymers4165
Water3,387188
1
A: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6894
Polymers14,4341
Non-polymers2553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5943
Polymers14,4341
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.434, 100.434, 103.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 14433.614 Da / Num. of mol.: 2 / Fragment: truncated LytM
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 5.26 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Tris, 2.0 M monoammonium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. all: 51861 / Num. obs: 51861 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 27.6
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2019 / Rsym value: 0.244 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QWY

1qwy


Resolution: 1.83→19.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.673 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The loop region A204-A210 breaks the crystallographic two-fold symmerty in P3(2)21 spacegroup, therefore it is modeled as double ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The loop region A204-A210 breaks the crystallographic two-fold symmerty in P3(2)21 spacegroup, therefore it is modeled as double conformation. Thus, if one conformation is chosen for one loop, then the other conformation is required for the symmetry mate.
RfactorNum. reflection% reflectionSelection details
Rfree0.19313 2599 5 %RANDOM
Rwork0.18069 ---
all0.18131 49103 --
obs0.18131 49103 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.468 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.83→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 17 188 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212091
X-RAY DIFFRACTIONr_bond_other_d00.021668
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9052847
X-RAY DIFFRACTIONr_angle_other_deg3.99733903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5965264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59824.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67915289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.571156
X-RAY DIFFRACTIONr_chiral_restr0.10.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022442
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02434
X-RAY DIFFRACTIONr_nbd_refined0.190.2352
X-RAY DIFFRACTIONr_nbd_other0.230.21446
X-RAY DIFFRACTIONr_nbtor_refined0.180.2986
X-RAY DIFFRACTIONr_nbtor_other0.1130.2954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5661.51635
X-RAY DIFFRACTIONr_mcbond_other0.0331.5561
X-RAY DIFFRACTIONr_mcangle_it1.68422053
X-RAY DIFFRACTIONr_scbond_it3.1493983
X-RAY DIFFRACTIONr_scangle_it3.6454.5794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 203 -
Rwork0.212 3582 -
obs--97.88 %

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