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- PDB-2w7u: SplA serine protease of Staphylococcus aureus (2.4A) -

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Basic information

Entry
Database: PDB / ID: 2w7u
TitleSplA serine protease of Staphylococcus aureus (2.4A)
ComponentsSERINE PROTEASE SPLA
KeywordsHYDROLASE / FAMILY S1
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan ...Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Serine proteases, trypsin domain / Trypsin / 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 SplA
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsStec-Niemczyka, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Popowicz, G.M. ...Stec-Niemczyka, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Popowicz, G.M. / Dubin, A. / Potempa, J. / Dubin, G.
Citation
Journal: Biochem.J. / Year: 2009
Title: Structural and Functional Characterization of Spla, an Exclusively Specific Protease of Staphylococcus Aureus.
Authors: Stec-Niemczyk, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Baczynski, K. / Popowicz, G.M. / ...Authors: Stec-Niemczyk, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Baczynski, K. / Popowicz, G.M. / Dubin, A. / Potempa, J. / Dubin, G.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Functional and Structural Characterization of Spl Proteases from Staphylococcus Aureus.
Authors: Popowicz, G.M. / Dubin, G. / Stec-Niemczyk, J. / Czarny, A. / Dubin, A. / Potempa, J. / Holak, T.A.
History
DepositionDec 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -5-STRANDED BARREL THIS IS REPRESENTED BY A -4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE PROTEASE SPLA
B: SERINE PROTEASE SPLA
C: SERINE PROTEASE SPLA
D: SERINE PROTEASE SPLA


Theoretical massNumber of molelcules
Total (without water)87,5424
Polymers87,5424
Non-polymers00
Water63135
1
A: SERINE PROTEASE SPLA


Theoretical massNumber of molelcules
Total (without water)21,8851
Polymers21,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE PROTEASE SPLA


Theoretical massNumber of molelcules
Total (without water)21,8851
Polymers21,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE PROTEASE SPLA


Theoretical massNumber of molelcules
Total (without water)21,8851
Polymers21,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE PROTEASE SPLA


Theoretical massNumber of molelcules
Total (without water)21,8851
Polymers21,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.994, 82.216, 134.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SERINE PROTEASE SPLA / SPLA SERINE PROTEASE


Mass: 21885.482 Da / Num. of mol.: 4 / Fragment: RESIDUES 36-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 8325-4 / Tissue: EXTRACELLULAR / Plasmid: PWB980 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800 / References: UniProt: Q2FXC2, glutamyl endopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.43 Å3/Da / Density % sol: 49.02 % / Description: NONE
Crystal growDetails: 0.2M SODIUM FORMATE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2007
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→20 Å / Num. obs: 30882 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AS9

2as9


Resolution: 2.43→19.87 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.406 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES AND SIDE CHAINS NOT DEFINED BY ELECTRON DENISTY WERE OMITTED FORM MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1559 5.1 %RANDOM
Rwork0.209 ---
obs0.211 29282 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.43→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5960 0 0 35 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6321.938248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3585793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.52925.62274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12415929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.272158
X-RAY DIFFRACTIONr_chiral_restr0.0470.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024708
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1530.32320
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.54095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.5347
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.339
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2571.53983
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92326285
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.732302
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0024.51963
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: 2.43→2.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 95
Rwork0.289 2070

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