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- PDB-6ruh: Ni-substituted alpha-Keggin bound to Proteinase K solved by MR -

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Basic information

Entry
Database: PDB / ID: 6ruh
TitleNi-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 space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ni-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 / refine_hist / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _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)34,5274
Polymers28,9591
Non-polymers5,5683
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.960, 67.960, 102.670
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-542-

HOH

21A-688-

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-WNI / Ni-substituted alpha-Keggin


Mass: 2735.884 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NiO39PW11
#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.: 349 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
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, 5 mM Ni-subsituted 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→30.39 Å / Num. obs: 184806 / % possible obs: 99.06 % / Redundancy: 3.4 % / CC1/2: 0.93 / Rmerge(I) obs: 0.2197 / Rpim(I) all: 0.1319 / Net I/σ(I): 4.83
Reflection shellResolution: 1.1→1.139 Å / Num. unique obs: 17305

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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→30.39 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 14.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1583 9217 4.99 %
Rwork0.1467 --
obs0.1473 184791 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→30.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 109 351 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012246
X-RAY DIFFRACTIONf_angle_d1.5413304
X-RAY DIFFRACTIONf_dihedral_angle_d12.236740
X-RAY DIFFRACTIONf_chiral_restr0.08317
X-RAY DIFFRACTIONf_plane_restr0.007376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1001-1.11260.18912770.18485240X-RAY DIFFRACTION88
1.1126-1.12570.19162910.1795542X-RAY DIFFRACTION94
1.1257-1.13940.18412900.17475661X-RAY DIFFRACTION96
1.1394-1.15380.17613040.16335759X-RAY DIFFRACTION97
1.1538-1.1690.16213040.1575842X-RAY DIFFRACTION99
1.169-1.1850.16733060.14935893X-RAY DIFFRACTION100
1.185-1.20190.16643090.14865904X-RAY DIFFRACTION100
1.2019-1.21990.17783080.14515908X-RAY DIFFRACTION100
1.2199-1.23890.16263120.1465904X-RAY DIFFRACTION100
1.2389-1.25920.15623090.14645927X-RAY DIFFRACTION100
1.2592-1.2810.18073090.14675922X-RAY DIFFRACTION100
1.281-1.30430.16053060.14915847X-RAY DIFFRACTION100
1.3043-1.32930.15323140.1455912X-RAY DIFFRACTION100
1.3293-1.35650.16463150.14235913X-RAY DIFFRACTION100
1.3565-1.3860.15163090.1385896X-RAY DIFFRACTION100
1.386-1.41820.13523110.13725893X-RAY DIFFRACTION100
1.4182-1.45370.14513150.13395892X-RAY DIFFRACTION100
1.4537-1.4930.15373040.13155914X-RAY DIFFRACTION100
1.493-1.53690.1363100.13175897X-RAY DIFFRACTION100
1.5369-1.58650.1443070.12925879X-RAY DIFFRACTION100
1.5865-1.64320.1543040.1325930X-RAY DIFFRACTION100
1.6432-1.7090.1333100.1345890X-RAY DIFFRACTION100
1.709-1.78680.14423160.13655934X-RAY DIFFRACTION100
1.7868-1.8810.14943120.1385865X-RAY DIFFRACTION100
1.881-1.99880.15483110.13915927X-RAY DIFFRACTION100
1.9988-2.15310.15243110.14175882X-RAY DIFFRACTION100
2.1531-2.36970.14723130.14625890X-RAY DIFFRACTION100
2.3697-2.71240.14853110.1515918X-RAY DIFFRACTION100
2.7124-3.41660.15743150.15385898X-RAY DIFFRACTION100
3.4166-30.57820.19423040.16645895X-RAY DIFFRACTION100

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