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- PDB-3i34: Proteinase K by LB Nanotemplate Method after high X-Ray dose on I... -

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Basic information

Entry
Database: PDB / ID: 3i34
TitleProteinase K by LB Nanotemplate Method after high X-Ray dose on ID14-2 Beamline at ESRF
ComponentsProteinase K
KeywordsHYDROLASE / Disulfide bond / 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 speciesTritirachium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsPechkova, E. / Tripathi, S.K. / Ravelli, R. / McSweeney, S. / Nicolini, C.
CitationJournal: To be Published
Title: Radiation damage study of Proteinase K at ID14-2 beamline at ESRF
Authors: Pechkova, E. / Tripathi, S.K. / Ravelli, R. / McSweeney, S. / Nicolini, C.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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)29,3724
Polymers28,9311
Non-polymers4413
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.865, 67.865, 102.335
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-439-

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) / Strain: Limber / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 385 / 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: 39.6 % / Mosaicity: 0.16 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20mg/mL in 25mM HEPES, pH7.0 PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2007 / Details: Mirror
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1→56.558 Å / Num. obs: 110313 / % possible obs: 83.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 12
Reflection shellResolution: 0.99→1.05 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.5 / Num. measured all: 10149 / Num. unique all: 6029 / % possible all: 31.9

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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
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTK

1ptk


Resolution: 1→23.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.879 / SU B: 0.45 / SU ML: 0.024 / SU R Cruickshank DPI: 0.036 / SU Rfree: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5279 5 %RANDOM
Rwork0.206 ---
obs0.206 105893 82.56 %-
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: 8.426 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 3 385 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212062
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9382804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08323.70481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5431511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021593
X-RAY DIFFRACTIONr_nbd_refined0.2190.31112
X-RAY DIFFRACTIONr_nbtor_refined0.3130.51463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.5549
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.384
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.589
X-RAY DIFFRACTIONr_mcbond_it0.62621387
X-RAY DIFFRACTIONr_mcangle_it1.08532176
X-RAY DIFFRACTIONr_scbond_it1.072764
X-RAY DIFFRACTIONr_scangle_it1.4523628
LS refinement shellResolution: 1.002→1.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.621 37 -
Rwork0.517 661 -
all-698 -
obs--7.47 %

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