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- PDB-7ln7: X-ray radiation damage series on Proteinase K at 277K, crystal st... -

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Basic information

Entry
Database: PDB / ID: 7ln7
TitleX-ray radiation damage series on Proteinase K at 277K, crystal structure, dataset 1
ComponentsProteinase K
KeywordsHYDROLASE / radiation damage / conformational heterogeneity / protease
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / 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. / Peptidase S8, subtilisin, Ser-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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsYabukarski, F. / Doukov, T. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.
Authors: Yabukarski, F. / Doukov, T. / Mokhtari, D.A. / Du, S. / Herschlag, D.
History
DepositionFeb 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,2875
Polymers28,9591
Non-polymers3284
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.820, 67.820, 101.865
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-503-

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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe residue at position 207 was modeled as aspartate instead of serine because the electron density ...The residue at position 207 was modeled as aspartate instead of serine because the electron density unambiguously indicates an aspartate at this position.

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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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Proteinase K was dissolved at a final concentration of 30 mg/ml in 10mM Calcium Chloride, 50 mM Tris pH 7.5. 1-2 microliters of this protein solution was mixed with an equivalent volume of ...Details: Proteinase K was dissolved at a final concentration of 30 mg/ml in 10mM Calcium Chloride, 50 mM Tris pH 7.5. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution from the well (1.0 M Ammonium Sulfate).

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.02→34.91 Å / Num. obs: 120801 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 8.87 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.038 / Net I/σ(I): 8.5
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5794 / Rpim(I) all: 0.862 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IC6

1ic6


Resolution: 1.02→33.91 Å / SU ML: 0.0942 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1381 5878 4.87 %
Rwork0.1228 114706 -
obs0.1235 120584 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.81 Å2
Refinement stepCycle: LAST / Resolution: 1.02→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 16 287 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632565
X-RAY DIFFRACTIONf_angle_d0.92313534
X-RAY DIFFRACTIONf_chiral_restr0.0757375
X-RAY DIFFRACTIONf_plane_restr0.0062489
X-RAY DIFFRACTIONf_dihedral_angle_d12.8487935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.31171890.30793598X-RAY DIFFRACTION95.63
1.03-1.040.28251740.28093784X-RAY DIFFRACTION99.45
1.04-1.060.26422080.2653738X-RAY DIFFRACTION99.77
1.06-1.070.23911980.24023764X-RAY DIFFRACTION99.9
1.07-1.080.22882000.22493790X-RAY DIFFRACTION99.92
1.08-1.10.23691980.21453770X-RAY DIFFRACTION99.9
1.1-1.110.21042070.1973784X-RAY DIFFRACTION99.75
1.11-1.130.22931940.19263780X-RAY DIFFRACTION99.7
1.13-1.150.18752290.17973744X-RAY DIFFRACTION100
1.15-1.170.18562080.16633783X-RAY DIFFRACTION100
1.17-1.190.16041840.15713802X-RAY DIFFRACTION100
1.19-1.210.17392000.14773778X-RAY DIFFRACTION99.97
1.21-1.230.14361910.1423804X-RAY DIFFRACTION99.97
1.23-1.260.1451850.14153820X-RAY DIFFRACTION100
1.26-1.290.15941860.13713804X-RAY DIFFRACTION99.97
1.29-1.320.14161950.1293813X-RAY DIFFRACTION99.9
1.32-1.350.15412160.12453768X-RAY DIFFRACTION100
1.35-1.380.13111780.10853845X-RAY DIFFRACTION99.93
1.38-1.430.12671870.10513804X-RAY DIFFRACTION100
1.43-1.470.10861800.0953864X-RAY DIFFRACTION100
1.47-1.520.11011910.09243824X-RAY DIFFRACTION100
1.52-1.580.12232030.0913826X-RAY DIFFRACTION100
1.58-1.660.10951760.09333873X-RAY DIFFRACTION100
1.66-1.740.11771790.09553873X-RAY DIFFRACTION100
1.74-1.850.12341740.0983875X-RAY DIFFRACTION100
1.85-20.10232300.09063856X-RAY DIFFRACTION100
2-2.20.11422120.08963874X-RAY DIFFRACTION100
2.2-2.520.10092160.09833894X-RAY DIFFRACTION100
2.52-3.170.13531890.11323979X-RAY DIFFRACTION99.98
3.17-33.910.12662010.11894195X-RAY DIFFRACTION100

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