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- PDB-4mvn: Crystal structure of the staphylococcal serine protease SplA in c... -

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Basic information

Entry
Database: PDB / ID: 4mvn
TitleCrystal structure of the staphylococcal serine protease SplA in complex with a specific phosphonate inhibitor
ComponentsSerine protease splA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CHYMOTRYPSIN-LIKE FOLD / SERINE ENDOPEPTIDASE / EXTRACELLULAR STAPHYLOCOCCAL PROTEASES / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
Chem-I1S / Serine protease SplA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZdzalik, M. / Burchacka, E. / Niemczyk, J.S. / Pustelny, K. / Popowicz, G.M. / Wladyka, B. / Dubin, A. / Potempa, J. / Sienczyk, M. / Dubin, G. / Oleksyszyn, J.
CitationJournal: Protein Sci. / Year: 2014
Title: Development and binding characteristics of phosphonate inhibitors of SplA protease from Staphylococcus aureus.
Authors: Burchacka, E. / Zdzalik, M. / Niemczyk, J.S. / Pustelny, K. / Popowicz, G. / Wladyka, B. / Dubin, A. / Potempa, J. / Sienczyk, M. / Dubin, G. / Oleksyszyn, J.
History
DepositionSep 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 8, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Serine protease splA
B: Serine protease splA
C: Serine protease splA
D: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8838
Polymers87,5424
Non-polymers1,3414
Water15,727873
1
A: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2212
Polymers21,8851
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2212
Polymers21,8851
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2212
Polymers21,8851
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2212
Polymers21,8851
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.131, 81.626, 133.787
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


Mass: 21885.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: SPLA, SAOUHSC_01942 / Production host: Bacillus subtilis (bacteria)
References: UniProt: Q2FXC2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-I1S / [(1S)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl]phosphonic acid


Mass: 335.292 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18NO5P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 873 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR FULL CHEMICAL FORMULA CBZ-PHE(P)(OC6H5-4-SO2CH3)2 IS HYDROLYSED BY THE PROTEASE (THAT ...THE INHIBITOR FULL CHEMICAL FORMULA CBZ-PHE(P)(OC6H5-4-SO2CH3)2 IS HYDROLYSED BY THE PROTEASE (THAT IS THE REACTION MECHANISM) AND ONLY THE PART CBZ-PHE(P) (LIGAND I1S) OF IT INTERACTS WITH THE PROTEIN.

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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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 0.2M CALCIUM CHLORIDE, 25% PEG 4000, PH 7.0, VAPOR DIFFUSION, TEMPERATURE 297K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 14, 2008
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 85873 / % possible obs: 96.7 %
Reflection shellResolution: 1.7→1.74 Å

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Processing

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

2w7s


Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.912 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4355 5.1 %RANDOM
Rwork0.165 ---
obs0.167 81518 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 88 873 6961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226351
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9488619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93625.76283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.683151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.239158
X-RAY DIFFRACTIONr_chiral_restr0.1670.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214907
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4491.53971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29126420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.31532380
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9514.52180
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 303 -
Rwork0.233 6038 -
obs--98.57 %

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