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- PDB-3ufa: Crystal structure of the staphylococcal serine protease SplA in c... -

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Basic information

Entry
Database: PDB / ID: 3ufa
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 protease / extracellular protease / 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
N-(3-CARBOXYPROPANOYL)-L-VALYL-N-[(1S)-2-PHENYL-1-PHOSPHONOETHYL]-L-PROLINAMIDE / Chem-VPF / Serine protease SplA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZdzalik, M. / Pietrusewicz, E. / Pustelny, K. / Stec-Niemczyk, J. / Popowicz, G.M. / Potempa, J. / Oleksyszyn, J. / Dubin, G.
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
DepositionOct 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8727
Polymers43,7712
Non-polymers1,1015
Water5,152286
1
A: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4183
Polymers21,8851
Non-polymers5332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease splA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4544
Polymers21,8851
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.232, 61.232, 221.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serine protease splA


Mass: 21885.482 Da / Num. of mol.: 2
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-VPF / N-(3-carboxypropanoyl)-L-valyl-N-[(1S)-2-phenyl-1-phosphonoethyl]-L-prolinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 497.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32N3O8P
References: N-(3-CARBOXYPROPANOYL)-L-VALYL-N-[(1S)-2-PHENYL-1-PHOSPHONOETHYL]-L-PROLINAMIDE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M HEPES, 20% PEG 4000, 10% Isopropanol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→53 Å / Num. obs: 42345

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.202 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23728 2127 5 %RANDOM
Rwork0.19045 ---
obs0.19288 40170 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.988 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 33 286 3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223186
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.9484310
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49325.683139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8815542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.667154
X-RAY DIFFRACTIONr_chiral_restr0.1560.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212424
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_it1.4351.51992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3223219
X-RAY DIFFRACTIONr_scbond_it3.36231194
X-RAY DIFFRACTIONr_scangle_it5.3414.51083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 116 -
Rwork0.32 2578 -
obs--85.8 %

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