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- PDB-6k8m: High resolution crystal structure of proteinase K with thiourea -

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Basic information

Entry
Database: PDB / ID: 6k8m
TitleHigh resolution crystal structure of proteinase K with thiourea
ComponentsProteinase K
KeywordsHYDROLASE / Serine protease / Thiourea / 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
THIOUREA / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAhmad, M.S. / Akbar, Z. / Choudhary, M.I.
CitationJournal: Bioorganic Chemistry / Year: 2019
Title: High resolution crystal structure of proteinase K with thiourea
Authors: Ahmad, M.S. / Akbar, Z. / Choudhary, M.I.
History
DepositionJun 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3196
Polymers28,9591
Non-polymers3605
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.842, 67.842, 102.377
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
11E-495-

HOH

21E-596-

HOH

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Components

#1: Protein Proteinase K / / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.838 Da / Num. of mol.: 1 / Mutation: S207D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Escherichia coli (E. coli) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-TOU / THIOUREA / Thiourea


Mass: 76.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4N2S / 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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 39.47 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 1.28M ammonium sulfate, 0.1M Tris-HCl, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.45→19.79 Å / Num. obs: 43099 / % possible obs: 99.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 14.42 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.092 / Χ2: 0.98 / Net I/av σ(I): 12.4 / Net I/σ(I): 12.4
Reflection shellResolution: 1.45→1.45 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2165 / Rrim(I) all: 0.787 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PEK

1pek


Resolution: 1.45→19.79 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 2162 5 %RANDOM
Rwork0.1682 ---
obs0.1688 40867 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 39.57 Å2 / Biso mean: 6.304 Å2 / Biso min: 2.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.45→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 18 226 2269
Biso mean--12.45 15.51 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132079
X-RAY DIFFRACTIONr_bond_other_d0.0380.0181815
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.6432824
X-RAY DIFFRACTIONr_angle_other_deg2.4791.5784197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72221.80994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86315297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6471512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022437
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02471
X-RAY DIFFRACTIONr_mcbond_it0.6070.5531115
X-RAY DIFFRACTIONr_mcbond_other0.570.5511114
X-RAY DIFFRACTIONr_mcangle_it0.8850.8281392
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 164 -
Rwork0.274 2936 -
all-3100 -
obs--99.49 %

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