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- PDB-7lpu: X-ray radiation damage series on Proteinase K at 277K, multi-conf... -

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Basic information

Entry
Database: PDB / ID: 7lpu
TitleX-ray radiation damage series on Proteinase K at 277K, multi-conformer model, 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. ...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 / 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 12, 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
Revision 1.3Nov 20, 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)29,2875
Polymers28,9591
Non-polymers3284
Water5,080282
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

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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.: 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


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of ...Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution (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: 0.0998 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.2409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1378 5878 4.87 %
Rwork0.1189 114706 -
obs0.1199 120584 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.97 Å2
Refinement stepCycle: LAST / Resolution: 1.02→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 16 282 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666457
X-RAY DIFFRACTIONf_angle_d0.95158740
X-RAY DIFFRACTIONf_chiral_restr0.0725978
X-RAY DIFFRACTIONf_plane_restr0.00661137
X-RAY DIFFRACTIONf_dihedral_angle_d12.29772225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.33991890.31183598X-RAY DIFFRACTION95.63
1.03-1.040.29031740.28173784X-RAY DIFFRACTION99.45
1.04-1.060.27522080.26673738X-RAY DIFFRACTION99.77
1.06-1.070.26071980.24283764X-RAY DIFFRACTION99.9
1.07-1.080.2352000.22963790X-RAY DIFFRACTION99.92
1.08-1.10.25331980.2193770X-RAY DIFFRACTION99.9
1.1-1.110.22842070.20333784X-RAY DIFFRACTION99.75
1.11-1.130.24281940.19473780X-RAY DIFFRACTION99.7
1.13-1.150.18642290.17813744X-RAY DIFFRACTION100
1.15-1.170.18682080.16893783X-RAY DIFFRACTION100
1.17-1.190.16891840.16013802X-RAY DIFFRACTION100
1.19-1.210.1762000.1533778X-RAY DIFFRACTION99.97
1.21-1.230.14891910.1483804X-RAY DIFFRACTION99.97
1.23-1.260.15361850.14393820X-RAY DIFFRACTION100
1.26-1.290.16591860.1393804X-RAY DIFFRACTION99.97
1.29-1.320.1481950.13133813X-RAY DIFFRACTION99.9
1.32-1.350.15522160.12363768X-RAY DIFFRACTION100
1.35-1.380.12911780.10953845X-RAY DIFFRACTION99.93
1.38-1.430.12371870.10813804X-RAY DIFFRACTION100
1.43-1.470.11791800.09523864X-RAY DIFFRACTION100
1.47-1.520.11591910.093824X-RAY DIFFRACTION100
1.52-1.580.11452030.08523826X-RAY DIFFRACTION100
1.58-1.660.10391760.08523873X-RAY DIFFRACTION100
1.66-1.740.09941790.08513873X-RAY DIFFRACTION100
1.74-1.850.10851740.08823875X-RAY DIFFRACTION100
1.85-20.10072300.08373856X-RAY DIFFRACTION100
2-2.20.11062120.08293874X-RAY DIFFRACTION100
2.2-2.520.09372160.0893894X-RAY DIFFRACTION100
2.52-3.170.12611890.10673979X-RAY DIFFRACTION99.98
3.17-33.910.13212010.11364195X-RAY DIFFRACTION100

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