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- PDB-7a68: proteinase K crystallized from 0.5 M NaNO3 -

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Basic information

Entry
Database: PDB / ID: 7a68
Titleproteinase K crystallized from 0.5 M NaNO3
ComponentsProteinase K
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / membrane
Similarity search - Function
: / VtrA C-terminal periplasmic domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Subtilase family / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Putative transcriptional regulator ToxR
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsIlina, K.B. / Kulikov, A.G. / Timofeev, V.I. / Marchenkova, M.A. / Pisarevsky, Y.V. / Kovalchuk, M.V.
CitationJournal: To Be Published
Title: proteinase K crystallized from 0.5 M NaNO3
Authors: Ilina, K.B. / Kulikov, A.G. / Timofeev, V.I. / Marchenkova, M.A. / Pisarevsky, Y.V. / Kovalchuk, M.V.
History
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,0053
Polymers28,9591
Non-polymers462
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area10600 Å2
Unit cell
Length a, b, c (Å)68.320, 68.320, 108.100
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-432-

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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein concentration: 10mg/ml. 0,2 M Tris pH 8, 0.5 M NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54184 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 8092 / % possible obs: 92.04 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.13 / Net I/σ(I): 5.8749
Reflection shellResolution: 2.55→2.69 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / Num. unique obs: 1199 / Rrim(I) all: 0.387

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ID8

2id8


Resolution: 2.55→28.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.873 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 416 5.2 %RANDOM
Rwork0.1468 ---
obs0.1496 7635 90.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.87 Å2 / Biso mean: 13.707 Å2 / Biso min: 1.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.55→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 2 68 2102
Biso mean--9.48 16.45 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171810
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6392847
X-RAY DIFFRACTIONr_angle_other_deg1.9351.5724221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1655280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10322.14398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6241512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 27 -
Rwork0.214 579 -
all-606 -
obs--95.89 %

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