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- PDB-4qpb: Catalytic domain of the antimicrobial peptidase lysostaphin from ... -

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Basic information

Entry
Database: PDB / ID: 4qpb
TitleCatalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the absence of phosphate
ComponentsLysostaphin
KeywordsHYDROLASE / Peptidase family M23 / Peptidoglycan amidase / Metallopeptidase / Peptidoglycan / Extracellular
Function / homology
Function and homology information


lysostaphin / cell wall organization / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Lysostaphin, N-terminal domain / Domain of unknown function (DUF6721) / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 ...Lysostaphin, N-terminal domain / Domain of unknown function (DUF6721) / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSabala, I. / Jagielska, E. / Bardelang, P.T. / Czapinska, H. / Dahms, S.O. / Sharpe, J.A. / James, R. / Than, M.E. / Thomas, N.R. / Bochtler, M.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans.
Authors: Sabala, I. / Jagielska, E. / Bardelang, P.T. / Czapinska, H. / Dahms, S.O. / Sharpe, J.A. / James, R. / Than, M.E. / Thomas, N.R. / Bochtler, M.
History
DepositionJun 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: Lysostaphin
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8695
Polymers30,6762
Non-polymers1933
Water4,270237
1
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4042
Polymers15,3381
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4663
Polymers15,3381
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.289, 107.318, 34.307
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysostaphin / Glycyl-glycine endopeptidase


Mass: 15338.175 Da / Num. of mol.: 2 / Fragment: catalytic domain, unp residues 248-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus simulans (bacteria) / Strain: Staphylococcus simulans bv. staphylolyticus / Gene: lss, U66883.1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10547, lysostaphin
#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 6 mM pentapeptide GGSGG, 0.1 M Tris (base), Bicine pH 8.5, 0.1 M amino acids (L-Na-glutamate, alanine (racemic), glycine; lysine-HCl (racemic); serine (racemic)), 30% v/v precipitant ...Details: 6 mM pentapeptide GGSGG, 0.1 M Tris (base), Bicine pH 8.5, 0.1 M amino acids (L-Na-glutamate, alanine (racemic), glycine; lysine-HCl (racemic); serine (racemic)), 30% v/v precipitant (ethylene glycol, PEG 8000)., VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.78→35 Å / Num. all: 23389 / Num. obs: 23389 / % possible obs: 99.1 % / Redundancy: 2.74 % / Rsym value: 0.167 / Net I/σ(I): 7.52
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3748 / Rsym value: 0.586 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4QP5

4qp5


Resolution: 1.78→33.99 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24432 707 3 %THIN RESOLUTION SHELLS
Rwork0.21025 ---
obs0.21133 23387 99.19 %-
all-23387 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.819 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20.02 Å2
2--1.61 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.78→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 6 237 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212214
X-RAY DIFFRACTIONr_bond_other_d00.021841
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9083007
X-RAY DIFFRACTIONr_angle_other_deg1.38834313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9045279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93724.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20215334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.563154
X-RAY DIFFRACTIONr_chiral_restr0.110.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212566
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02478
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_it1.0431.51347
X-RAY DIFFRACTIONr_mcbond_other01.5580
X-RAY DIFFRACTIONr_mcangle_it1.68422152
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6793867
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9324.5855
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.779→1.875 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.333 105 -
Rwork0.321 3304 -
obs--99.04 %

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