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- PDB-5mjl: Single-shot pink beam serial crystallography: Proteinase K -

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Basic information

Entry
Database: PDB / ID: 5mjl
TitleSingle-shot pink beam serial crystallography: Proteinase K
ComponentsProteinase K
KeywordsHYDROLASE / Proteinase K / Serial Crystallography / Pink beam
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/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
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21013789926 Å
AuthorsMeents, A. / Oberthuer, D. / Lieske, J. / Srajer, V.
Funding support5items
OrganizationGrant numberCountry
European Cluster of Advanced Laser Light Sources (EUCALL)
Virtual Institute, Helmholtz AssociationVH-VI-403
Advanced Photon Source, a U.S. Department of Energy (DOE), Argonne National LaboratoryDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM111072
Philip Anfinrud (NIH/NIDDK)NSF award 1231306
Citation
Journal: Nat Commun / Year: 2017
Title: Pink-beam serial crystallography.
Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / ...Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / Ogata, C.M. / Kissick, D.J. / Taft, M.H. / Manstein, D.J. / Lieske, J. / Oberthuer, D. / Fischetti, R.F. / Chapman, H.N.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,4805
Polymers28,9591
Non-polymers5214
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-12 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 68.300, 108.300
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

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Protein , 1 types, 1 molecules A

#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.) Engyodontium album (fungus) / Gene: PROK / Production host: Engyodontium album (fungus) / References: UniProt: P06873, peptidase K

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Non-polymers , 5 types, 326 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 1.6M MgSO4, 10 mM CaCl2, 100 mM CHC buffer pH 6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.1-1.3
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jul 10, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.31
ReflectionResolution: 2.1→100 Å / Num. obs: 9197 / % possible obs: 57.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 0.0186601051545 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.5
Reflection shellResolution: 2.21→2.31 Å / Redundancy: 15.31 % / Num. measured obs: 6356 / % possible all: 26.06

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_9999phasing
PHENIX1.10.1-2155_9999refinement
Precognition/Epinorm (RenzResearch)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AVJ

5avj


Resolution: 2.21013789926→44.1083574029 Å / SU ML: 0.179507088267 / Cross valid method: FREE R-VALUE / σ(F): 0.416332133786 / Phase error: 11.9910233688
RfactorNum. reflection% reflection
Rfree0.194518100148 792 9.49526435679 %
Rwork0.153604213342 --
obs0.157478947888 8341 62.1303538175 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 6.34427693799 Å2
Refinement stepCycle: LAST / Resolution: 2.21013789926→44.1083574029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 30 322 2384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002110676146852151
X-RAY DIFFRACTIONf_angle_d0.5706028194032932
X-RAY DIFFRACTIONf_chiral_restr0.0403263001001319
X-RAY DIFFRACTIONf_plane_restr0.00208668177934384
X-RAY DIFFRACTIONf_dihedral_angle_d9.977172871481274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2101-2.34860.219700539108830.171922755875698X-RAY DIFFRACTION35.908045977
2.3486-2.52990.223763368357910.163260919253867X-RAY DIFFRACTION43.8845625286
2.5299-2.78450.2135489518411070.1726640135841111X-RAY DIFFRACTION55.6164383562
2.7845-3.18730.2204638649921410.1638660346251369X-RAY DIFFRACTION68.2331676457
3.1873-4.01520.1721820988851770.1366379893821681X-RAY DIFFRACTION81.9585355095
4.0152-44.11710.16842223481930.1438353136621823X-RAY DIFFRACTION84.6347607053

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