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- PDB-4qp5: Catalytic domain of the antimicrobial peptidase lysostaphin from ... -

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Basic information

Entry
Database: PDB / ID: 4qp5
TitleCatalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the presence of phosphate
ComponentsLysostaphin
KeywordsHYDROLASE / Peptidase family M23 / Peptidoglycan amidase / Metallopeptidase / Peptidoglycan / Extracellular
Function / homology
Function and homology information


lysostaphin / cell wall organization / metallopeptidase 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 / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 ...Lysostaphin, N-terminal domain / Domain of unknown function (DUF6721) / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / SH3-like domain, bacterial-type / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Lysostaphin
Similarity search - Component
Biological speciesStaphylococcus simulans bv. staphylolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 16, 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_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_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)31,1818
Polymers30,6762
Non-polymers5056
Water3,945219
1
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5914
Polymers15,3381
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5914
Polymers15,3381
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.279, 106.780, 34.331
Angle α, β, γ (deg.)90.00, 97.42, 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 bv. staphylolyticus (bacteria)
Gene: 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M potassium dihydrogen phosphate, 20 % w/v PEG 8000 and 6 mM glycine hydroxamate supplemented with 10% (v/v) glycerol for cryocooling. Crystal was soaked for 5 min with 25 mM iodo-GGSGG ...Details: 0.05 M potassium dihydrogen phosphate, 20 % w/v PEG 8000 and 6 mM glycine hydroxamate supplemented with 10% (v/v) glycerol for cryocooling. Crystal was soaked for 5 min with 25 mM iodo-GGSGG pentapeptide dissolved in the buffer used for cryocooling, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.20001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.20001 Å / Relative weight: 1
ReflectionResolution: 1.26→35.6 Å / Num. obs: 64943 / % possible obs: 98.3 % / Redundancy: 5.77 % / Rsym value: 0.072 / Net I/σ(I): 13.23
Reflection shellResolution: 1.26→1.33 Å / Redundancy: 4.47 % / Mean I/σ(I) obs: 2.49 / Rsym value: 0.412 / % possible all: 90.9

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LXC

4lxc


Resolution: 1.26→34.04 Å / σ(F): 1.42 / Phase error: 26.75 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.175 2039 3.14 %
Rwork0.13 --
obs0.133 64902 98.3 %
all-64902 -
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.91 Å2 / ksol: 0.54 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9557 Å20 Å21.0607 Å2
2--3.6445 Å2-0 Å2
3----1.6888 Å2
Refinement stepCycle: LAST / Resolution: 1.26→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 24 219 2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012359
X-RAY DIFFRACTIONf_angle_d1.1533220
X-RAY DIFFRACTIONf_dihedral_angle_d12.654847
X-RAY DIFFRACTIONf_chiral_restr0.074304
X-RAY DIFFRACTIONf_plane_restr0.005427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2679-1.29890.30721850.20883791X-RAY DIFFRACTION85
1.2989-1.33310.23281030.20574409X-RAY DIFFRACTION98
1.3331-1.37130.24311460.19824392X-RAY DIFFRACTION97
1.3713-1.41420.2171620.19124191X-RAY DIFFRACTION94
1.4142-1.46310.16961030.17384392X-RAY DIFFRACTION98
1.4631-1.51950.2232060.1674319X-RAY DIFFRACTION95
1.5195-1.58580.20141030.15754356X-RAY DIFFRACTION98
1.5858-1.66540.16231030.15294405X-RAY DIFFRACTION98
1.6654-1.76390.15862070.14864300X-RAY DIFFRACTION95
1.7639-1.89070.15821050.14034416X-RAY DIFFRACTION98
1.8907-2.06420.18141050.12744403X-RAY DIFFRACTION98
2.0642-2.32630.17222010.12164317X-RAY DIFFRACTION96
2.3263-2.8080.14141020.11554421X-RAY DIFFRACTION98
2.808-4.51020.16941980.09154339X-RAY DIFFRACTION96

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