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- PDB-3de1: Proteinase K by LB nanotemplate method after the third step of hi... -

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Basic information

Entry
Database: PDB / ID: 3de1
TitleProteinase K by LB nanotemplate method after the third step of high X-Ray dose on ESRF ID23-1 beamline
ComponentsProteinase K
KeywordsHYDROLASE / Alpha Beta protein / Calcium / Metal-binding / Protease / Serine protease / Zymogen
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
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPechkova, E. / Tripathi, S.K. / Nicolini, C.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Radiation stability of proteinase K crystals grown by LB nanotemplate method
Authors: Pechkova, E. / Tripathi, S. / Ravelli, R.B. / McSweeney, S. / Nicolini, C.
History
DepositionJun 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 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_special_symmetry / 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 9, 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)67.669, 67.669, 101.625
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-415-

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) Engyodontium album (fungus) / Strain: Limber / 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: 2.01 Å3/Da / Density % sol: 38.82 % / Mosaicity: 0.38 °
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 microL of protein ...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 microL of protein solution with 4 microL of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→56.344 Å / Num. obs: 14864 / % possible obs: 90.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.1 / Num. measured all: 11004 / Num. unique all: 2130 / Rsym value: 0.258 / % possible all: 90.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DE0

3de0


Resolution: 2→34.84 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.229 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 734 5 %RANDOM
Rwork0.181 ---
obs0.182 14826 89.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 1 198 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212062
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9382804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37123.70481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1115296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3911511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021593
X-RAY DIFFRACTIONr_nbd_refined0.2320.31114
X-RAY DIFFRACTIONr_nbtor_refined0.3160.51451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.5304
X-RAY DIFFRACTIONr_metal_ion_refined1.3790.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4430.373
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5130.534
X-RAY DIFFRACTIONr_mcbond_it1.00821393
X-RAY DIFFRACTIONr_mcangle_it1.5632176
X-RAY DIFFRACTIONr_scbond_it1.4652767
X-RAY DIFFRACTIONr_scangle_it1.9783628
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 51 -
Rwork0.16 1017 -
all-1068 -
obs--90.05 %

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