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- PDB-5kxv: Structure Proteinase K at 0.98 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5kxv
TitleStructure Proteinase K at 0.98 Angstroms
ComponentsProteinase K
KeywordsHYDROLASE / Serine Protease / hydrolysis / aminolysis / catalytic triad
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
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsMasuda, T. / Suzuki, M. / Inoue, S. / Numata, K. / Sugahara, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology25650026 Japan
CitationJournal: Sci Rep / Year: 2017
Title: Atomic resolution structure of serine protease proteinase K at ambient temperature.
Authors: Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Nakane, T. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Mikami, B. / Nureki, O. / Numata, K. / ...Authors: Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Nakane, T. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Mikami, B. / Nureki, O. / Numata, K. / Iwata, S. / Sugahara, M.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_mutation / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2856
Polymers28,9591
Non-polymers3265
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.577, 67.577, 107.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-706-

HOH

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Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH (P2308) / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5 / Details: 250 mM NaNO3, 50 mM CaCl2, 50 mM MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 141433 / % possible obs: 99.5 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 58.41
Reflection shellResolution: 0.98→1 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 6.47 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5L

4b5l


Resolution: 0.98→16.894 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 7.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.114 6943 4.91 %Random
Rwork0.1002 ---
obs0.1009 141318 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.98→16.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 18 434 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062441
X-RAY DIFFRACTIONf_angle_d0.9673370
X-RAY DIFFRACTIONf_dihedral_angle_d13.485890
X-RAY DIFFRACTIONf_chiral_restr0.08357
X-RAY DIFFRACTIONf_plane_restr0.007468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9802-0.99130.12672080.1374405X-RAY DIFFRACTION99
0.9913-1.0030.15092300.13374391X-RAY DIFFRACTION99
1.003-1.01520.13442320.1194402X-RAY DIFFRACTION99
1.0152-1.0280.1162060.11614452X-RAY DIFFRACTION99
1.028-1.04160.12992460.11124392X-RAY DIFFRACTION99
1.0416-1.05580.1262160.10544456X-RAY DIFFRACTION100
1.0558-1.07090.10932280.10034423X-RAY DIFFRACTION100
1.0709-1.08690.10172400.09364422X-RAY DIFFRACTION100
1.0869-1.10390.09092320.09224409X-RAY DIFFRACTION100
1.1039-1.1220.11082300.0884476X-RAY DIFFRACTION100
1.122-1.14130.09152340.08574430X-RAY DIFFRACTION100
1.1413-1.16210.08822120.08144471X-RAY DIFFRACTION100
1.1621-1.18440.09362530.08084431X-RAY DIFFRACTION100
1.1844-1.20860.09462320.08024492X-RAY DIFFRACTION100
1.2086-1.23480.09352160.08224445X-RAY DIFFRACTION100
1.2348-1.26360.09122320.08554447X-RAY DIFFRACTION100
1.2636-1.29510.11072010.0844539X-RAY DIFFRACTION100
1.2951-1.33020.09772560.08534441X-RAY DIFFRACTION100
1.3302-1.36930.10172220.08514485X-RAY DIFFRACTION100
1.3693-1.41350.11052600.08454484X-RAY DIFFRACTION100
1.4135-1.46390.10222460.08494451X-RAY DIFFRACTION100
1.4639-1.52250.09552440.08124504X-RAY DIFFRACTION100
1.5225-1.59180.09392500.0844488X-RAY DIFFRACTION100
1.5918-1.67560.09472180.08924537X-RAY DIFFRACTION100
1.6756-1.78050.10822450.09474534X-RAY DIFFRACTION100
1.7805-1.91780.12672150.10064527X-RAY DIFFRACTION100
1.9178-2.11050.11742350.0994560X-RAY DIFFRACTION99
2.1105-2.41510.1142120.10444577X-RAY DIFFRACTION99
2.4151-3.03990.12152450.11534567X-RAY DIFFRACTION99
3.0399-16.89680.14222470.12184737X-RAY DIFFRACTION97

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