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- PDB-4inl: Crystal structure of SplD protease from Staphylococcus aureus at ... -

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Basic information

Entry
Database: PDB / ID: 4inl
TitleCrystal structure of SplD protease from Staphylococcus aureus at 2.1 A resolution
ComponentsSerine protease SplD
KeywordsHYDROLASE / chymotrypsin-like protease / serine endopeptidase / extracellular staphylococcal proteases
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease SplD
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCichon, P. / Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Wladyka, B. / Daugherty, P.S. ...Cichon, P. / Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Wladyka, B. / Daugherty, P.S. / Lesner, A. / Rolka, K. / Dubin, A. / Potempa, J. / Dubin, G.
CitationJournal: Plos One / Year: 2013
Title: Biochemical and Structural Characterization of SplD Protease from Staphylococcus aureus.
Authors: Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Cichon, P. / Stach, N. / Gruba, N. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Kedracka-Krok, S. / Wladyka, B. / ...Authors: Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Cichon, P. / Stach, N. / Gruba, N. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Kedracka-Krok, S. / Wladyka, B. / Daugherty, P.S. / Lesner, A. / Rolka, K. / Dubin, A. / Potempa, J. / Dubin, G.
History
DepositionJan 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease SplD


Theoretical massNumber of molelcules
Total (without water)22,1821
Polymers22,1821
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.273, 174.273, 174.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21A-363-

HOH

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Components

#1: Protein Serine protease SplD


Mass: 22181.920 Da / Num. of mol.: 1 / Fragment: UNP residues 37-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_01938, splD / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FXC5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.1→26.27 Å / Num. obs: 11885 / % possible obs: 86.7 % / Redundancy: 3 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 3.1 / % possible all: 72.1

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Processing

Software
NameVersionClassification
PHASERphasing
Cootmodel building
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W7S

2w7s


Resolution: 2.1→24.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.831 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25578 574 4.8 %RANDOM
Rwork0.2118 ---
obs0.21391 11303 86.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.587 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 0 66 1569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9512094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81825.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.015153
X-RAY DIFFRACTIONr_chiral_restr0.10.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211165
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2624
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21028
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9481.51028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52921621
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.463583
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6284.5473
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 28 -
Rwork0.286 582 -
obs--67.48 %

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