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- PDB-3d9q: Proteinase K by LB nanotemplate method before high X-Ray dose on ... -

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Basic information

Entry
Database: PDB / ID: 3d9q
TitleProteinase K by LB nanotemplate method before high X-Ray dose on ESRF ID23-1 beamline
ComponentsProteinase K
KeywordsHYDROLASE / Proteinase K / LB nanotemplate / 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 / molecular replacement / Resolution: 1.43 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
DepositionMay 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 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 1.3Nov 6, 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)67.760, 67.760, 101.609
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) / Genus: PROK / 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: 2.02 Å3/Da / Density % sol: 38.98 % / Mosaicity: 0.25 °
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 2007 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.426→56.375 Å / Num. obs: 32221 / % possible obs: 72.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.8
Reflection shellResolution: 1.43→1.5 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.3 / Num. measured all: 1690 / Num. unique all: 1344 / Rsym value: 0.485 / % possible all: 21.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTK

1ptk


Resolution: 1.43→40.65 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.907 / SU B: 1.257 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1613 5 %RANDOM
Rwork0.211 ---
obs0.213 32156 71.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.43→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 1 198 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212062
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9382804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5415278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00123.70481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42815296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8671511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021593
X-RAY DIFFRACTIONr_nbd_refined0.2290.31119
X-RAY DIFFRACTIONr_nbtor_refined0.3180.51460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.5312
X-RAY DIFFRACTIONr_metal_ion_refined0.340.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4530.380
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4890.534
X-RAY DIFFRACTIONr_mcbond_it0.73221389
X-RAY DIFFRACTIONr_mcangle_it1.20232176
X-RAY DIFFRACTIONr_scbond_it1.1092764
X-RAY DIFFRACTIONr_scangle_it1.563628
LS refinement shellResolution: 1.426→1.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 16 -
Rwork0.283 321 -
all-337 -
obs--10.42 %

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