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Basic information

Entry
Database: PDB / ID: 2prk
TitleSYNCHROTRON X-RAY DATA COLLECTION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF PROTEINASE K AT 1.5 ANGSTROMS RESOLUTION
ComponentsPROTEINASE K
KeywordsSERINE PROTEINASE
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 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 / Resolution: 1.5 Å
AuthorsBetzel, C. / Pal, G.P. / Saenger, W.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution.
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
#1: Journal: FEBS Lett. / Year: 1986
Title: Crystallization of the Bifunctional Proteinase/Amylase Inhibitor Pki-3 and of its Complex with Proteinase K
Authors: Pal, G.P. / Betzel, C. / Jany, K.-D. / Saenger, W.
#2: Journal: FEBS Lett. / Year: 1986
Title: Active-Site Geometry of Proteinase K. Crystallographic Study of its Complex with a Dipeptide Chloromethyl Ketone Inhibitor
Authors: Betzel, C. / Pal, G.P. / Struck, M. / Jany, K.-D. / Saenger, W.
#3: Journal: Embo J. / Year: 1984
Title: Three-Dimensional Structure of Fungal Proteinase K Reveals Similarity to Bacterial Subtilisin
Authors: Paehler, A. / Banerjee, A. / Dattagupta, J.K. / Fujiwara, T. / Lindner, K. / Pal, G.P. / Suck, D. / Weber, G. / Saenger, W.
#4: Journal: J.Mol.Biol. / Year: 1975
Title: Crystallization of the Fungal Enzyme Proteinase K and Amino Acid Composition
Authors: Dattagupta, J.K. / Fujiwara, T. / Grishin, E.V. / Lindner, K. / Manor, P.C. / Pieniazek, N.J. / Saenger, W. / Suck, D.
History
DepositionNov 30, 1987Processing site: BNL
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0113
Polymers28,9311
Non-polymers802
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.170, 68.170, 108.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUE 171 IS A CIS PROLINE.

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Components

#1: Protein PROTEINASE K


Mass: 28930.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Engyodontium album (fungus) / References: UniProt: P06873, 3.4.21.14
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 178 / 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

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal grow
*PLUS
pH: 6.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %protein1drop
250 mMTris-HCl1reservoir2-amino-2-(hydroxymethyl)-1,3-propanediol
310 mM1reservoirCaCl2
41 M1reservoirNaNO3
50.02 %1reservoirNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 10694 / Observed criterion σ(I): 3 / Num. measured all: 36039 / Rmerge(I) obs: 0.081

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.167 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 2 178 2197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.9
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 3 / Highest resolution: 1.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 30812 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.027
X-RAY DIFFRACTIONp_planar_d0.0370.043
X-RAY DIFFRACTIONp_plane_restr0.020.012
X-RAY DIFFRACTIONp_chiral_restr0.10.146
X-RAY DIFFRACTIONp_mcbond_it10.849
X-RAY DIFFRACTIONp_scbond_it11.452
X-RAY DIFFRACTIONp_mcangle_it1.51.234
X-RAY DIFFRACTIONp_scangle_it1.52.195

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