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- PDB-3ti7: Crystal structure of the basic protease BprV from the ovine footr... -

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Basic information

Entry
Database: PDB / ID: 3ti7
TitleCrystal structure of the basic protease BprV from the ovine footrot pathogen, Dichelobacter nodosus
ComponentsBasic extracellular subtilisin-like protease BprV
KeywordsHYDROLASE
Function / homology
Function and homology information


serine-type endopeptidase activity / metal ion binding
Similarity search - Function
Peptidase MprA-like catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Peptidase MprA-like catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Galactose-binding-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Basic extracellular subtilisin-like protease BprV
Similarity search - Component
Biological speciesDichelobacter nodosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWong, W. / Whisstock, J.C. / Porter, C.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: S1 Pocket of a Bacterially Derived Subtilisin-like Protease Underpins Effective Tissue Destruction.
Authors: Wong, W. / Wijeyewickrema, L.C. / Kennan, R.M. / Reeve, S.B. / Steer, D.L. / Reboul, C. / Smith, A.I. / Pike, R.N. / Rood, J.I. / Whisstock, J.C. / Porter, C.J.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal / Item: _exptl_crystal.density_percent_sol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic extracellular subtilisin-like protease BprV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0614
Polymers36,9411
Non-polymers1203
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.497, 89.637, 47.654
Angle α, β, γ (deg.)90.000, 113.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Basic extracellular subtilisin-like protease BprV


Mass: 36940.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dichelobacter nodosus (bacteria) / Strain: VCS1703A / Gene: bpr, bprV, DNO_0605 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: A5EVD0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 3350, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→44.81 Å / Num. all: 20048 / Num. obs: 20018 / Limit h max: 17 / Limit h min: -19 / Limit k max: 44 / Limit k min: 0 / Limit l max: 23 / Limit l min: 0
Reflection scaleGroup code: 1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.724 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.866 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1022 5.1 %RANDOM
Rwork0.1627 ---
obs0.166 20018 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.15 Å2 / Biso mean: 16.1343 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.12 Å2
2---0.93 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 2→27.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 3 312 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212544
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9283466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06524.324111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59815364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6231516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022001
X-RAY DIFFRACTIONr_nbd_refined0.1980.21323
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21738
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2242
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.218
X-RAY DIFFRACTIONr_mcbond_it0.82521705
X-RAY DIFFRACTIONr_mcangle_it1.652657
X-RAY DIFFRACTIONr_scbond_it3.1137961
X-RAY DIFFRACTIONr_scangle_it4.18510809
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 95 -
Rwork0.199 1338 -
all-1433 -
obs--97.95 %

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