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- PDB-7ltd: X-ray radiation damage series on Proteinase K at 100K, crystal st... -

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Basic information

Entry
Database: PDB / ID: 7ltd
TitleX-ray radiation damage series on Proteinase K at 100K, 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 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/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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 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 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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)29,3097
Polymers28,9591
Non-polymers3506
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.721, 67.721, 101.423
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY
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. This is consistent with other high-resolution crystal structures with 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: 2.01 Å3/Da / Density % sol: 38.74 %
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 (0.5 M Sodium Nitrate).

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Data collection

DiffractionMean temperature: 100 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: 0.9→34.82 Å / Num. obs: 173186 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 5.85 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.029 / Net I/σ(I): 10.3
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1 / Num. unique obs: 7909 / Rpim(I) all: 0.519 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LN7

7ln7


Resolution: 0.9→33.86 Å / SU ML: 0.0917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172 8457 4.89 %
Rwork0.1574 164573 -
obs0.1582 173030 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.99 Å2
Refinement stepCycle: LAST / Resolution: 0.9→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 21 461 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542586
X-RAY DIFFRACTIONf_angle_d0.89933558
X-RAY DIFFRACTIONf_chiral_restr0.0744379
X-RAY DIFFRACTIONf_plane_restr0.0059498
X-RAY DIFFRACTIONf_dihedral_angle_d12.9486939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.910.3242740.33574854X-RAY DIFFRACTION89.53
0.91-0.920.33562460.29645361X-RAY DIFFRACTION98.01
0.92-0.930.27452860.26615381X-RAY DIFFRACTION99.7
0.93-0.940.26762990.24815445X-RAY DIFFRACTION99.93
0.94-0.960.25342760.24245458X-RAY DIFFRACTION99.97
0.96-0.970.24632890.23365452X-RAY DIFFRACTION99.98
0.97-0.980.2432720.23065475X-RAY DIFFRACTION99.91
0.98-10.24872750.21755430X-RAY DIFFRACTION99.93
1-1.010.22842820.21515444X-RAY DIFFRACTION100
1.01-1.030.25062810.21155474X-RAY DIFFRACTION99.98
1.03-1.050.22172710.20675449X-RAY DIFFRACTION99.97
1.05-1.070.20662870.1965458X-RAY DIFFRACTION100
1.07-1.090.20042980.19225458X-RAY DIFFRACTION99.93
1.09-1.110.19472930.18025466X-RAY DIFFRACTION100
1.11-1.130.19562920.17395447X-RAY DIFFRACTION100
1.13-1.160.1743030.16755448X-RAY DIFFRACTION100
1.16-1.190.17962790.16585497X-RAY DIFFRACTION100
1.19-1.220.16252830.15795482X-RAY DIFFRACTION99.98
1.22-1.260.18272800.15845513X-RAY DIFFRACTION100
1.26-1.30.15572590.15245513X-RAY DIFFRACTION100
1.3-1.340.16663130.15085463X-RAY DIFFRACTION100
1.34-1.40.17592630.15355534X-RAY DIFFRACTION100
1.4-1.460.17062600.14635537X-RAY DIFFRACTION99.97
1.46-1.540.15422790.13525564X-RAY DIFFRACTION100
1.54-1.640.15822830.13615525X-RAY DIFFRACTION100
1.64-1.760.152380.13985620X-RAY DIFFRACTION100
1.76-1.940.16043050.13845593X-RAY DIFFRACTION100
1.94-2.220.14483100.13065585X-RAY DIFFRACTION100
2.22-2.80.13882910.12795674X-RAY DIFFRACTION99.98
2.8-33.860.14032900.13295973X-RAY DIFFRACTION99.98

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