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- PDB-6qf1: X-Ray structure of Proteinase K crystallized on a silicon chip -

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Basic information

Entry
Database: PDB / ID: 6qf1
TitleX-Ray structure of Proteinase K crystallized on a silicon chip
ComponentsProteinase K
KeywordsHYDROLASE / Proteinase K / on-chip crystallization / in-situ crystallization / room-temperature
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 / molecular replacement / Resolution: 1.737 Å
AuthorsLieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. ...Lieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
Funding support Germany, Sweden, United States, 6items
OrganizationGrant numberCountry
European Research Council609920 Germany
European UnionHorizon 2020, No. 654220 Germany
German Federal Ministry for Education and Research05K2018-2017-06727MXD Germany
Swedish Research Council2010-5208 Sweden
Swedish Research Council2012-2849 Sweden
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Iucrj / Year: 2019
Title: On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies.
Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. ...Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 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 1.2Mar 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 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,2063
Polymers28,9591
Non-polymers2472
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-7 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.467, 68.467, 108.272
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-465-

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 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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M CHC buffer pH 6.5, 0.6M ammonium sulphate, 10mM calcium chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.737→44.196 Å / Num. obs: 27136 / % possible obs: 99.6 % / Redundancy: 11.1 % / Biso Wilson estimate: 13.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.15 / Net I/σ(I): 10.9
Reflection shellResolution: 1.737→1.77 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1465 / CC1/2: 0.921 / Rrim(I) all: 0.677 / % possible all: 99.9
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: humidity stream / Sample holding: single crystalline silicon chip / Support base: goniometer

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.24data extraction
PHENIX1.10.1-2155_9999refinement
Coot0.8.2model building
PHASERphasing
Aimless0.5.8data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5L

4b5l


Resolution: 1.737→44.196 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.94
RfactorNum. reflection% reflection
Rfree0.1558 1995 7.37 %
Rwork0.1335 --
obs0.1351 27060 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.23 Å2 / Biso mean: 17.6097 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.737→44.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 30 190 2252
Biso mean--92.47 30.72 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052272
X-RAY DIFFRACTIONf_angle_d0.7463135
X-RAY DIFFRACTIONf_chiral_restr0.049346
X-RAY DIFFRACTIONf_plane_restr0.005417
X-RAY DIFFRACTIONf_dihedral_angle_d10.5631413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7366-1.780.21351400.184517651905100
1.78-1.82810.20051400.178217431883100
1.8281-1.88190.21731400.16117721912100
1.8819-1.94270.16531430.155117801923100
1.9427-2.01210.16111410.136817691910100
2.0121-2.09260.1711390.14291761190099
2.0926-2.18790.1531430.13617921935100
2.1879-2.30320.1741420.12971782192499
2.3032-2.44750.16751410.130417851926100
2.4475-2.63650.14241440.1331801194599
2.6365-2.90170.15011430.13131780192399
2.9017-3.32150.15141420.12391808195098
3.3215-4.18420.11551440.11071820196498
4.1842-44.21070.15221530.1311907206096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1681-0.2397-0.03981.517-0.28011.04730.02310.21260.0103-0.0768-0.02280.18410.017-0.1528-0.00710.0818-0.0004-0.00350.1804-0.02330.110981.52550.3377102.7737
22.4253-3.52042.30026.7948-3.83053.35580.0028-0.1624-0.28920.29710.15760.35680.135-0.1288-0.17710.119-0.03280.0240.1247-0.00830.146583.572240.2863116.2561
32.8479-1.69120.25673.4965-1.39832.2947-0.0659-0.0542-0.08830.10750.02650.08410.0671-0.11430.03550.0569-0.04930.0130.0899-0.02680.109784.441743.3794110.7278
46.6204-0.24432.35793.34031.63679.18710.06730.10750.04390.0471-0.04650.05750.0931-0.0014-0.07220.08310.00760.00980.05780.0010.124997.840736.1801111.0954
51.1852-0.5357-0.29481.62330.521.63730.0263-0.01790.07690.07910.0096-0.12980.09690.0526-0.03440.0793-0.0032-0.00390.1003-0.00310.101199.35548.5201111.8398
61.26740.1095-0.04631.08750.33090.88450.0182-0.00230.13620.0714-0.03590.0344-0.0523-0.04820.00540.08450.01140.00170.0994-0.00390.110686.837756.746111.4748
71.48280.2951-0.32623.39431.72332.8440.040.23060.3138-0.15040.0297-0.1024-0.1674-0.0367-0.04430.0951-0.0030.01650.140.05990.158295.455862.0822101.0504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 78 )A59 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 103 )A79 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 120 )A104 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 183 )A121 - 183
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 239 )A184 - 239
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 279 )A240 - 279

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