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- PDB-4lxc: The antimicrobial peptidase lysostaphin from Staphylococcus simulans -

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Basic information

Entry
Database: PDB / ID: 4lxc
TitleThe antimicrobial peptidase lysostaphin from Staphylococcus simulans
ComponentsLysostaphin
KeywordsHYDROLASE / PEPTIDASE FAMILY M23 / PEPTIDOGLYCAN HYDROLASE / METALLOPEPTIDASE / PEPTIDOGLYCAN
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 / SH3 Domains / Distorted Sandwich / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Other
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 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_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Lysostaphin
B: Lysostaphin
C: Lysostaphin
D: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,83617
Polymers112,7104
Non-polymers1,12613
Water0
1
A: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4354
Polymers28,1781
Non-polymers2583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5315
Polymers28,1781
Non-polymers3544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2432
Polymers28,1781
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6276
Polymers28,1781
Non-polymers4505
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Lysostaphin
B: Lysostaphin
hetero molecules

C: Lysostaphin
D: Lysostaphin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,83617
Polymers112,7104
Non-polymers1,12613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_555-z+1/4,-y+1/4,-x+1/41
Buried area9370 Å2
ΔGint-296 kcal/mol
Surface area44400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.013, 282.013, 282.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAAA278 - 38532 - 139
21METMETALAALABB278 - 38532 - 139
31METMETALAALACC278 - 38532 - 139
41METMETALAALADD278 - 38532 - 139
12LYSLYSLYSLYSAA403 - 493157 - 247
22LYSLYSLYSLYSBB403 - 493157 - 247
32LYSLYSLYSLYSCC403 - 493157 - 247
42LYSLYSLYSLYSDD403 - 493157 - 247

NCS ensembles :
ID
1
2

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Components

#1: Protein
Lysostaphin / / Glycyl-glycine endopeptidase


Mass: 28177.551 Da / Num. of mol.: 4 / Fragment: unp residues 248-493
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

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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: 8.29 Å3/Da / Density % sol: 85.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES and 1.6 M magnesium sulphate, 2 mM tetraglycine phosphinic acid. EDTA and ammonium sulphate as additives improved crystal quality, pH 6.5, 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: 0.918409 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2013
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 48693 / Num. obs: 48693 / % possible obs: 100 % / Redundancy: 36.4 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.295 / Rsym value: 0.295 / Net I/σ(I): 17.34
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 37.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 5.34 / Num. unique all: 3539 / Rsym value: 0.908 / % possible all: 100

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Processing

Software
NameVersionClassification
CBFlibdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1R77, 2B0P

1r77

2b0p


Resolution: 3.5→47.67 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.796 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS AND TLS REFINEMENT HAS BEEN USED. DEPENDING ON THE RESOLUTION CUTOFF WE OBSERVED A WILSON B VALUE IN THE RANGE OF 30 AND 80 AND KEPT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS AND TLS REFINEMENT HAS BEEN USED. DEPENDING ON THE RESOLUTION CUTOFF WE OBSERVED A WILSON B VALUE IN THE RANGE OF 30 AND 80 AND KEPT THE ATOMIC B AT A FIXED VALUE OF 36 OBSERVED FOR THE DEPOSITED DATA CUTOFF.
RfactorNum. reflection% reflectionSelection details
Rfree0.28684 2435 5 %RANDOM
Rwork0.26777 ---
obs0.26873 48689 100 %-
all-48689 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.566 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7540 0 49 0 7589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217822
X-RAY DIFFRACTIONr_bond_other_d00.025182
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.92310623
X-RAY DIFFRACTIONr_angle_other_deg4.421312593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96923.795332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.977151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8191524
X-RAY DIFFRACTIONr_chiral_restr0.0660.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028781
X-RAY DIFFRACTIONr_gen_planes_other0.0350.021647
X-RAY DIFFRACTIONr_nbd_refined0.2110.21693
X-RAY DIFFRACTIONr_nbd_other0.2310.25073
X-RAY DIFFRACTIONr_nbtor_refined0.1950.23728
X-RAY DIFFRACTIONr_nbtor_other0.1180.23822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.54769
X-RAY DIFFRACTIONr_mcbond_other01.52029
X-RAY DIFFRACTIONr_mcangle_it027653
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it033053
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it04.52970
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1412medium positional1.270.5
12B1412medium positional0.620.5
13C1412medium positional0.710.5
14D1412medium positional0.520.5
21A1217medium positional0.390.5
22B1217medium positional0.280.5
23C1217medium positional0.340.5
24D1217medium positional0.350.5
11A1412medium thermal02
12B1412medium thermal02
13C1412medium thermal02
14D1412medium thermal02
21A1217medium thermal02
22B1217medium thermal02
23C1217medium thermal02
24D1217medium thermal02
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 162 -
Rwork0.304 3371 -
obs-3533 99.97 %
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)
17.83261.3968-1.96695.11971.23087.6882-0.0527-0.5427-0.3860.00580.1473-0.2949-0.44280.1956-0.0946-0.34250.10220.1897-0.20180.0048-0.243462.69160.3899.911
26.90850.8367-0.12585.2525-0.04246.02940.05040.2341-0.02160.0348-0.14460.3174-0.1379-0.03180.0942-0.44450.04460.0573-0.4653-0.0692-0.343876.92138.984-37.336
312.143-0.4425-3.64516.2427-1.40799.3435-0.5714-0.0029-2.1458-0.0822-0.09660.6850.4359-0.25410.668-0.21110.10210.3583-0.36230.06510.349236.99141.6667.705
45.3725-0.0607-0.83346.0934-0.44475.2265-0.3208-0.1613-0.35760.13490.10470.30520.2901-0.03810.2161-0.36250.0690.1554-0.4118-0.0059-0.427977.96313.398-19.344
514.61672.889-3.96114.0204-0.11649.19220.20620.8431.36880.11280.10170.2334-0.6667-0.3823-0.3079-0.25190.14830.0625-0.24260.1409-0.241770.02768.663-27.012
65.52141.6436-2.34278.05430.34757.42460.05790.85510.1207-0.3467-0.30360.8036-0.3883-0.97770.2456-0.37510.1140.0614-0.1097-0.0532-0.097847.157.145-20.196
77.92412.1008-1.31268.4317-2.31766.03120.14960.48690.2662-0.19850.27990.7712-0.0709-0.8718-0.4296-0.41790.0587-0.0361-0.2078-0.0112-0.171446.76927.756-28.133
89.6508-1.4176-3.73113.0166-0.65819.0875-0.5436-0.4664-0.69730.02290.2880.73410.5019-0.53240.2556-0.2086-0.07060.0709-0.10870.04470.060939.48812.956-7.616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A248 - 370
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B254 - 370
4X-RAY DIFFRACTION2B601
5X-RAY DIFFRACTION3C249 - 370
6X-RAY DIFFRACTION3C601
7X-RAY DIFFRACTION4D249 - 370
8X-RAY DIFFRACTION4D601
9X-RAY DIFFRACTION5A395 - 480
10X-RAY DIFFRACTION6B395 - 480
11X-RAY DIFFRACTION7C395 - 480
12X-RAY DIFFRACTION8D395 - 480

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