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- PDB-3dvr: Proteinase K by LB nanotemplate method after the first step of hi... -

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Basic information

Entry
Database: PDB / ID: 3dvr
TitleProteinase K by LB nanotemplate method after the first step of high X-Ray dose on ESRF ID14-2 beamline
ComponentsProteinase K
KeywordsHYDROLASE / alpha and beta proteins / Calcium / Metal-binding / Protease / Serine protease / Zymogen
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
Biological speciesTritirachium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsPechkova, E. / Tripathi, S.K. / Nicolini, C.
CitationJournal: To be Published
Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective
Authors: Pechkova, E. / Tripathi, S.K. / Nicolini, C.
History
DepositionJul 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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
X: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9712
Polymers28,9311
Non-polymers401
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.963, 67.963, 102.196
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
11X-431-

HOH

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Components

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


Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tritirachium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.04 Å3/Da / Density % sol: 39.69 % / Mosaicity: 0.46 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20mg/ml of protein in 25mM HEPES pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microlitres of ...Details: 20mg/ml of protein in 25mM HEPES pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microlitres of protein solution with 4 microlitres of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2007 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.02→56.614 Å / Num. obs: 99190 / % possible obs: 82.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.2
Reflection shellResolution: 1.02→1.08 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.5 / Num. measured all: 8365 / Num. unique all: 5181 / Rsym value: 0.302 / % possible all: 30.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTK

1ptk


Resolution: 1.02→56.61 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.887 / SU B: 0.363 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4952 5 %RANDOM
Rwork0.207 ---
obs0.207 99153 82.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 8.058 Å2 / Biso min: 2.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.02→56.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 1 198 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212062
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9382804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4095278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46123.70481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38815296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9321511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021593
X-RAY DIFFRACTIONr_nbd_refined0.2510.31112
X-RAY DIFFRACTIONr_nbtor_refined0.3170.51457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.5332
X-RAY DIFFRACTIONr_metal_ion_refined0.2850.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4440.375
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5540.537
X-RAY DIFFRACTIONr_mcbond_it0.67321384
X-RAY DIFFRACTIONr_mcangle_it1.13632176
X-RAY DIFFRACTIONr_scbond_it1.0272764
X-RAY DIFFRACTIONr_scangle_it1.4153628
LS refinement shellResolution: 1.025→1.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 70 -
Rwork0.347 1586 -
all-1656 -
obs--18.92 %

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