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- PDB-9fty: Serial microseconds crystallography at ID29 using fixed-target (s... -

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Basic information

Entry
Database: PDB / ID: 9fty
TitleSerial microseconds crystallography at ID29 using fixed-target (small foils): Proteinase K with 20 um spacing between X-ray pulses
ComponentsProteinase K
KeywordsHYDROLASE / Serial crystallography / serial microsecond crystallography / room temperature / ID29 / ESRF-EBS
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 / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOrlans, J. / Rose, S.L. / Basu, S. / de Sanctis, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2025
Title: Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.
Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez ...Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez Marrero, M. / Felisaz, F. / Papp, G. / Gonzalez, H. / Caserotto, H. / Dobias, F. / Gigmes, J. / Lebon, G. / Basu, S. / de Sanctis, D.
History
DepositionJun 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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)29,1014
Polymers28,9591
Non-polymers1423
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.720, 68.720, 108.970
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-635-

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
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Komagataella pastoris (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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.5 M sodium nitrate, 0.1 M calcium chloride

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Mar 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→58.13 Å / Num. obs: 18372 / % possible obs: 100 % / Redundancy: 133 % / Biso Wilson estimate: 17.29 Å2 / CC star: 0.9653 / R split: 0.3207 / Net I/σ(I): 3.94
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 889 / CC star: 0.7465 / R split: 1.2812
Serial crystallography sample deliveryDescription: small foils / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→58.13 Å / SU ML: 0.3049 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2622 1823 9.99 %
Rwork0.2403 16428 -
obs0.2425 18251 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.87 Å2
Refinement stepCycle: LAST / Resolution: 2→58.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 6 173 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152031
X-RAY DIFFRACTIONf_angle_d0.42142767
X-RAY DIFFRACTIONf_chiral_restr0.0403312
X-RAY DIFFRACTIONf_plane_restr0.0031365
X-RAY DIFFRACTIONf_dihedral_angle_d10.52683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.37591380.3531242X-RAY DIFFRACTION99.78
2.05-2.110.37611400.32251247X-RAY DIFFRACTION99.57
2.11-2.180.32081360.30231217X-RAY DIFFRACTION99.63
2.18-2.260.3141370.26391240X-RAY DIFFRACTION99.93
2.26-2.350.29521380.25931243X-RAY DIFFRACTION99.93
2.35-2.460.29371380.25941247X-RAY DIFFRACTION99.86
2.46-2.590.2721390.2521249X-RAY DIFFRACTION99.86
2.59-2.750.25861390.24081263X-RAY DIFFRACTION99.57
2.75-2.960.23641400.24561248X-RAY DIFFRACTION99.86
2.96-3.260.26941410.22981271X-RAY DIFFRACTION99.72
3.26-3.730.24581380.20821276X-RAY DIFFRACTION99.51
3.73-4.70.19331430.1881295X-RAY DIFFRACTION99.24
4.7-58.130.2141560.21661390X-RAY DIFFRACTION99.23

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