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- PDB-6qxv: Pink beam serial crystallography: Proteinase K, 1 us exposure, 15... -

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Basic information

Entry
Database: PDB / ID: 6qxv
TitlePink beam serial crystallography: Proteinase K, 1 us exposure, 1585 patterns merged (2 chips)
ComponentsProteinase K
KeywordsHYDROLASE / pink beam / fixed-target / serial crystallography / proteinase K
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/S53 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/S53 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsTolstikova, A. / Oberthuer, D. / Meents, A.
Funding support Germany, 5items
OrganizationGrant numberCountry
European Commission637295
German Federal Ministry for Education and Research031B0405D Germany
European Research Council609920
European Union654220
German Federal Ministry for Education and Research05K2018 - 2017-06727 Germany
CitationJournal: Iucrj / Year: 2019
Title: 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector.
Authors: Tolstikova, A. / Levantino, M. / Yefanov, O. / Hennicke, V. / Fischer, P. / Meyer, J. / Mozzanica, A. / Redford, S. / Crosas, E. / Opara, N.L. / Barthelmess, M. / Lieske, J. / Oberthuer, D. ...Authors: Tolstikova, A. / Levantino, M. / Yefanov, O. / Hennicke, V. / Fischer, P. / Meyer, J. / Mozzanica, A. / Redford, S. / Crosas, E. / Opara, N.L. / Barthelmess, M. / Lieske, J. / Oberthuer, D. / Wator, E. / Mohacsi, I. / Wulff, M. / Schmitt, B. / Chapman, H.N. / Meents, A.
History
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: 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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,20217
Polymers28,9591
Non-polymers1,24316
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-188 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.620, 68.620, 104.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

21A-570-

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 genetically manipulated source
Details: S312D mutation / Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M CHC buffer pH 6.6, 0.7M ammonium sulphate and 10mM calcium chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.80580-0.8262
DetectorType: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.80581
20.82621
ReflectionResolution: 1.94→21.7 Å / Num. obs: 18492 / % possible obs: 96.25 % / Redundancy: 23.1 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 0.8763 / Net I/σ(I): 4.6
Reflection shellResolution: 1.94→2.009 Å / CC1/2: 0.7166
Serial crystallography sample deliveryDescription: Roadrunner II / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Roadrunner II

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KXV

5kxv


Resolution: 1.94→21.7 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1
RfactorNum. reflection% reflection
Rfree0.2269 1767 9.59 %
Rwork0.1702 --
obs0.1756 18429 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.6 Å2 / Biso mean: 26.0448 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.94→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 60 187 2279
Biso mean--66.62 37.35 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.99240.3058970.233289399069
1.9924-2.0510.27641230.21681171129489
2.051-2.11720.2691320.18151247137997
2.1172-2.19280.22811370.17241297143499
2.1928-2.28050.23771370.153812941431100
2.2805-2.38410.22651390.151213131452100
2.3841-2.50970.20351390.15481306144599
2.5097-2.66660.2021400.156413081448100
2.6666-2.87210.24321400.161713341474100
2.8721-3.16030.22341400.16213271467100
3.1603-3.61580.19941430.148813491492100
3.6158-4.54870.18051460.145713731519100
4.5487-21.70090.27091540.213714501604100

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