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- PDB-6ruw: Zn-substituted alpha-Keggin bound to Proteinase K solved by MR -

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Basic information

Entry
Database: PDB / ID: 6ruw
TitleZn-substituted alpha-Keggin bound to Proteinase K solved by MR
ComponentsProteinase K
KeywordsPROTEIN BINDING / Polyoxometalate / Complex / alpha-Keggin / 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
Zn-substituted alpha-Keggin / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBreibeck, J. / Bijelic, A. / Rompel, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP27534 Austria
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Transition metal-substituted Keggin polyoxotungstates enabling covalent attachment to proteinase K upon co-crystallization.
Authors: Breibeck, J. / Bijelic, A. / Rompel, A.
History
DepositionMay 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 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_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id

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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)31,7973
Polymers28,9591
Non-polymers2,8392
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.920, 67.920, 102.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-587-

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-KK5 / Zn-substituted alpha-Keggin


Mass: 2742.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O39PW11Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium acetate (pH 5.5), 0.7-1.2 M ammonium sulphate, 2.5 mM Zn-substituted alpha-Keggin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.35→24.04 Å / Num. obs: 92760 / % possible obs: 92.48 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03601 / Rpim(I) all: 0.01637 / Net I/σ(I): 27.53
Reflection shellResolution: 1.35→1.398 Å / Num. unique obs: 8059

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IC6

1ic6


Resolution: 1.35→24.04 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 17.54
RfactorNum. reflection% reflection
Rfree0.1806 4645 5.01 %
Rwork0.1481 --
obs0.1497 92750 92.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 57 415 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052166
X-RAY DIFFRACTIONf_angle_d0.8053073
X-RAY DIFFRACTIONf_dihedral_angle_d14.108735
X-RAY DIFFRACTIONf_chiral_restr0.068316
X-RAY DIFFRACTIONf_plane_restr0.005375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36540.2861230.20512300X-RAY DIFFRACTION73
1.3654-1.38140.2411340.1872644X-RAY DIFFRACTION83
1.3814-1.39830.24281460.17072712X-RAY DIFFRACTION86
1.3983-1.4160.24681470.16422789X-RAY DIFFRACTION87
1.416-1.43460.21711430.17682708X-RAY DIFFRACTION87
1.4346-1.45430.23781450.17642778X-RAY DIFFRACTION87
1.4543-1.4750.2011540.16312834X-RAY DIFFRACTION88
1.475-1.49710.20791500.17782773X-RAY DIFFRACTION88
1.4971-1.52040.20661490.16252817X-RAY DIFFRACTION89
1.5204-1.54540.21811500.1742845X-RAY DIFFRACTION89
1.5454-1.5720.21961490.17482843X-RAY DIFFRACTION90
1.572-1.60060.20731510.16382864X-RAY DIFFRACTION91
1.6006-1.63140.19781530.16152886X-RAY DIFFRACTION91
1.6314-1.66470.20761530.15812930X-RAY DIFFRACTION92
1.6647-1.70090.20131520.15272923X-RAY DIFFRACTION92
1.7009-1.74040.20081550.15222930X-RAY DIFFRACTION93
1.7404-1.78390.2231550.15432985X-RAY DIFFRACTION94
1.7839-1.83210.19411590.14973014X-RAY DIFFRACTION94
1.8321-1.8860.15951600.14933034X-RAY DIFFRACTION95
1.886-1.94690.16171580.1473045X-RAY DIFFRACTION96
1.9469-2.01640.17061610.13573049X-RAY DIFFRACTION97
2.0164-2.09710.19751680.13153081X-RAY DIFFRACTION98
2.0971-2.19250.15431670.12973176X-RAY DIFFRACTION99
2.1925-2.3080.15951640.12823125X-RAY DIFFRACTION99
2.308-2.45250.16291660.13113173X-RAY DIFFRACTION100
2.4525-2.64160.16371680.13893149X-RAY DIFFRACTION100
2.6416-2.9070.1661630.13813202X-RAY DIFFRACTION100
2.907-3.32680.15131570.13263175X-RAY DIFFRACTION100
3.3268-4.18780.15351720.12293167X-RAY DIFFRACTION100
4.1878-24.04770.16381730.18033154X-RAY DIFFRACTION99

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