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- PDB-3de7: Proteinase K by Classical hanging drop method after the fourth st... -

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Basic information

Entry
Database: PDB / ID: 3de7
TitleProteinase K by Classical hanging drop method after the fourth 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 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 speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 8, 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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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, 102.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 2.05 Å3/Da / Density % sol: 40.05 % / 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 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: 2.3→56.705 Å / Num. obs: 11070 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.173 / Rsym value: 0.173 / Net I/σ(I): 3.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1 / Num. measured all: 7489 / Num. unique all: 1614 / Rsym value: 0.639 / % possible all: 99.9

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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 / Resolution: 2.3→35.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.988 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 527 4.8 %RANDOM
Rwork0.161 ---
obs0.163 11059 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 1 198 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212062
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9382804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65623.70481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96415296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.211511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021593
X-RAY DIFFRACTIONr_nbd_refined0.2280.31027
X-RAY DIFFRACTIONr_nbtor_refined0.3170.51450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.5258
X-RAY DIFFRACTIONr_metal_ion_refined2.0680.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.530.531
X-RAY DIFFRACTIONr_mcbond_it1.49621389
X-RAY DIFFRACTIONr_mcangle_it2.35632176
X-RAY DIFFRACTIONr_scbond_it1.8632768
X-RAY DIFFRACTIONr_scangle_it2.7623628
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 39 -
Rwork0.173 781 -
all-820 -
obs--99.76 %

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