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- PDB-2vid: Serine protease SplB from Staphylococcus aureus at 1.8A resolution -

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Basic information

Entry
Database: PDB / ID: 2vid
TitleSerine protease SplB from Staphylococcus aureus at 1.8A resolution
ComponentsSERINE PROTEASE SPLB
KeywordsHYDROLASE / PROTEASE / SERINE PROTEASE / STAPHYLOCOCCUS AUREUS
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 SplB / Serine protease SplB
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. ...Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. / Phopaisarn, M. / Daugherty, P.S. / Thogersen, I.B. / Enghild, J.J. / Thornberry, N. / Dubin, A. / Potempa, J.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Enzymatic Activity of the Staphylococcus Aureus Splb Serine Protease is Induced by Substrates Containing the Sequence Trp-Glu-Leu-Gln.
Authors: Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. / Phopaisarn, M. / Daugherty, P.S. / ...Authors: Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. / Phopaisarn, M. / Daugherty, P.S. / Thogersen, I.B. / Enghild, J.J. / Thornberry, N. / Dubin, A. / Potempa, J.
#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
DepositionNov 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" AND "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 "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-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 SPLB
B: SERINE PROTEASE SPLB


Theoretical massNumber of molelcules
Total (without water)44,8042
Polymers44,8042
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-18.9 kcal/mol
Surface area20030 Å2
MethodPQS
2
A: SERINE PROTEASE SPLB


Theoretical massNumber of molelcules
Total (without water)22,4021
Polymers22,4021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: SERINE PROTEASE SPLB


Theoretical massNumber of molelcules
Total (without water)22,4021
Polymers22,4021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.475, 117.475, 73.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SERINE PROTEASE SPLB / SPLB SERINE PROTEASE


Mass: 22402.086 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 8325-4 / Plasmid: PWB980 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800 / References: UniProt: Q9KH50, UniProt: Q2FXC3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.69 Å3/Da / Density % sol: 53.96 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP VAPOR DIFFUSION; 20C; GROWN BY MIXING EQUAL VOLUMES OF SPLB (35 MG/ML IN 5MM TRIS-HCL, PH 8.0 CONTAINING 50MM NACL) AND 0.1M TRIS-HCL, PH 8.5-9.0 CONTAINING 30% PEG 3350 ...Details: SITTING DROP VAPOR DIFFUSION; 20C; GROWN BY MIXING EQUAL VOLUMES OF SPLB (35 MG/ML IN 5MM TRIS-HCL, PH 8.0 CONTAINING 50MM NACL) AND 0.1M TRIS-HCL, PH 8.5-9.0 CONTAINING 30% PEG 3350 (OPTIMIZED HAMPTON RESEARCH INDEX SOLUTION NUMBER 45)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 48001 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AS9

2as9


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.834 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE EXCLUDED FROM THE MODEL. AUTHOR SUGGESTS TO RETAIN THE ORIGINAL WATERS AND NOT TO MOVE THEM TO SYMMETRY RELATED POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2403 5 %RANDOM
Rwork0.211 ---
obs0.213 45454 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 0 322 3354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223098
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9424202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3324.741135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20315484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1051510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21428
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22123
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2337
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0931.52013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80423188
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61431217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7364.51014
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 197
Rwork0.274 3277

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