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- PDB-3dvs: Proteinase K by LB nanotmplate method after the second step of hi... -

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Basic information

Entry
Database: PDB / ID: 3dvs
TitleProteinase K by LB nanotmplate method after the second step of high 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. / McSweeney, S. / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)67.986, 67.986, 102.248
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: 39.76 % / Mosaicity: 0.5 °
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: 98762 / % possible obs: 82 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 7.9
Reflection shellResolution: 1.02→1.08 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 1.4 / Num. measured all: 8026 / Num. unique all: 5003 / Rsym value: 0.534 / % possible all: 29.4

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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: 0.938 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.872 / SU B: 0.462 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4993 5.1 %RANDOM
Rwork0.22 ---
obs0.22 98715 81.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.84 Å2 / Biso mean: 9.351 Å2 / Biso min: 2.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 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_d0.0060.0212062
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9382804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23423.70481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89815296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9751511
X-RAY DIFFRACTIONr_chiral_restr0.080.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021593
X-RAY DIFFRACTIONr_nbd_refined0.220.31086
X-RAY DIFFRACTIONr_nbtor_refined0.3160.51465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5318
X-RAY DIFFRACTIONr_metal_ion_refined0.130.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4010.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3260.531
X-RAY DIFFRACTIONr_mcbond_it0.77921386
X-RAY DIFFRACTIONr_mcangle_it1.31132176
X-RAY DIFFRACTIONr_scbond_it1.1612764
X-RAY DIFFRACTIONr_scangle_it1.5993628
LS refinement shellResolution: 1.022→1.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 95 -
Rwork0.445 1308 -
all-1403 -
obs--15.89 %

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