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- PDB-6rug: Co-substituted alpha-Keggin bound to Proteinase K solved by MR -

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Basic information

Entry
Database: PDB / ID: 6rug
TitleCo-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 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
Co-substituted alpha-Keggin / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 28, 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 / refine / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 16, 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)34,5274
Polymers28,9591
Non-polymers5,5683
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 67.860, 102.300
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-579-

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: Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-WCO / Co-substituted alpha-Keggin


Mass: 2736.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoO39PW11
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.51 %
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 Co-substituted alpha-Keggin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.1→35 Å / Num. obs: 184016 / % possible obs: 99.33 % / Redundancy: 4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.1743 / Rpim(I) all: 0.09364 / Net I/σ(I): 5.04
Reflection shellResolution: 1.1→1.139 Å / Num. unique obs: 737740

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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: 1.1→34.996 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 14.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1545 9201 5 %
Rwork0.1442 --
obs0.1447 184012 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→34.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 109 304 2430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012228
X-RAY DIFFRACTIONf_angle_d1.5653278
X-RAY DIFFRACTIONf_dihedral_angle_d14.479732
X-RAY DIFFRACTIONf_chiral_restr0.078314
X-RAY DIFFRACTIONf_plane_restr0.007372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1002-1.11270.30932760.29495236X-RAY DIFFRACTION89
1.1127-1.12580.29222960.26955614X-RAY DIFFRACTION96
1.1258-1.13950.26242960.24445709X-RAY DIFFRACTION98
1.1395-1.15390.24533000.21985812X-RAY DIFFRACTION99
1.1539-1.16910.21653170.19845881X-RAY DIFFRACTION100
1.1691-1.18510.19633050.18535807X-RAY DIFFRACTION100
1.1851-1.20210.18493090.17145860X-RAY DIFFRACTION100
1.2021-1.220.19133090.16995864X-RAY DIFFRACTION100
1.22-1.23910.18813070.16795884X-RAY DIFFRACTION100
1.2391-1.25940.18313090.16555802X-RAY DIFFRACTION100
1.2594-1.28110.18823190.16295937X-RAY DIFFRACTION100
1.2811-1.30440.18163040.15875824X-RAY DIFFRACTION100
1.3044-1.32950.1673080.15125883X-RAY DIFFRACTION100
1.3295-1.35660.15173080.14645858X-RAY DIFFRACTION100
1.3566-1.38610.16873130.1365884X-RAY DIFFRACTION100
1.3861-1.41840.13353110.12565860X-RAY DIFFRACTION100
1.4184-1.45380.1373060.11885844X-RAY DIFFRACTION100
1.4538-1.49310.12243040.11545813X-RAY DIFFRACTION100
1.4931-1.53710.1423090.11345892X-RAY DIFFRACTION100
1.5371-1.58670.12533100.11395862X-RAY DIFFRACTION100
1.5867-1.64340.13593050.11135857X-RAY DIFFRACTION100
1.6434-1.70920.12133160.11545910X-RAY DIFFRACTION100
1.7092-1.7870.13753070.11945866X-RAY DIFFRACTION100
1.787-1.88120.13143140.12135832X-RAY DIFFRACTION100
1.8812-1.9990.13823020.12495897X-RAY DIFFRACTION100
1.999-2.15340.1223130.13175853X-RAY DIFFRACTION100
2.1534-2.370.12493030.13795874X-RAY DIFFRACTION100
2.37-2.71290.15923070.14395870X-RAY DIFFRACTION100
2.7129-3.41750.14833060.14365863X-RAY DIFFRACTION100
3.4175-35.01340.15933120.15455863X-RAY DIFFRACTION100

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