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- PDB-8sqv: Proteinase K Multiconformer Model at 333K -

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Basic information

Entry
Database: PDB / ID: 8sqv
TitleProteinase K Multiconformer Model at 333K
ComponentsProteinase K
KeywordsHYDROLASE / serine hydrolase / subtilisin-like / metal ion binding / a/b three-layered sandwiches
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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. ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsDu, S. / Wankowicz, S. / Yabukarski, F. / Doukov, T. / Herschlag, D. / Fraser, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145238 United States
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Methods Enzymol. / Year: 2023
Title: Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.
Authors: Du, S. / Wankowicz, S.A. / Yabukarski, F. / Doukov, T. / Herschlag, D. / Fraser, J.S.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3836
Polymers28,9591
Non-polymers4245
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.068, 68.068, 103.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Proteinase K was dissolved at pH 7.5 to 30 mg/mL in a 50 mM TRIS buffer . The protein was crystallized using a hanging drop setup on a 24 well VDX plate with sealant and 22 mm thick ...Details: Proteinase K was dissolved at pH 7.5 to 30 mg/mL in a 50 mM TRIS buffer . The protein was crystallized using a hanging drop setup on a 24 well VDX plate with sealant and 22 mm thick siliconized circle cover slides by mixing equal amounts of protein solution with ammonium sulfate.

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Data collection

DiffractionMean temperature: 333 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.03316 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.22→35.21 Å / Num. obs: 72388 / % possible obs: 94.21 % / Redundancy: 7.1 % / Biso Wilson estimate: 12.04 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 11.29
Reflection shellResolution: 1.22→1.264 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 5444 / CC1/2: 0.305 / CC star: 0.683 / % possible all: 76.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→35.21 Å / SU ML: 0.1382 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.5135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1687 2000 2.92 %
Rwork0.1315 66444 -
obs0.1325 68444 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.09 Å2
Refinement stepCycle: LAST / Resolution: 1.22→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 21 159 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727933
X-RAY DIFFRACTIONf_angle_d1.03610863
X-RAY DIFFRACTIONf_chiral_restr0.07661194
X-RAY DIFFRACTIONf_plane_restr0.01191454
X-RAY DIFFRACTIONf_dihedral_angle_d12.45292775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.31161130.25073753X-RAY DIFFRACTION75.58
1.25-1.280.28271180.24773913X-RAY DIFFRACTION78.88
1.28-1.320.28391180.23133932X-RAY DIFFRACTION79.43
1.32-1.370.27161360.23314514X-RAY DIFFRACTION90.84
1.37-1.410.26941470.21864871X-RAY DIFFRACTION97.87
1.41-1.470.26751490.19474963X-RAY DIFFRACTION99.71
1.47-1.540.1871500.16514987X-RAY DIFFRACTION99.96
1.54-1.620.19711500.14994999X-RAY DIFFRACTION99.96
1.62-1.720.19521520.13995017X-RAY DIFFRACTION99.88
1.72-1.850.15281510.11585029X-RAY DIFFRACTION99.88
1.85-2.040.12961520.09825039X-RAY DIFFRACTION99.92
2.04-2.330.12681530.0955086X-RAY DIFFRACTION99.75
2.33-2.940.13971530.11235091X-RAY DIFFRACTION99.04
2.94-35.210.14911580.11485250X-RAY DIFFRACTION97.34

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