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- PDB-2pkc: CRYSTAL STRUCTURE OF CALCIUM-FREE PROTEINASE K AT 1.5 ANGSTROMS R... -

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Entry
Database: PDB / ID: 2pkc
TitleCRYSTAL STRUCTURE OF CALCIUM-FREE PROTEINASE K AT 1.5 ANGSTROMS RESOLUTION
ComponentsPROTEINASE K
KeywordsHYDROLASE(SERINE PROTEINASE)
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/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / 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. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / 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
AuthorsMueller, A. / Hinrichs, W. / Wolf, W.M. / Saenger, W.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Crystal structure of calcium-free proteinase K at 1.5-A resolution.
Authors: Muller, A. / Hinrichs, W. / Wolf, W.M. / Saenger, W.
#1: Journal: Nature / Year: 1989
Title: Long-Range Structural Changes in Proteinase K Triggered by Calcium Ion Removal
Authors: Bajorath, J. / Raghunathan, S. / Hinrichs, W. / Saenger, W.
#2: Journal: Eur.J.Biochem. / Year: 1986
Title: Three-Dimensional Structure of Proteinase K at 0.15-Nm Resolution
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
History
DepositionJun 4, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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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)28,9542
Polymers28,9311
Non-polymers231
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.270, 68.270, 108.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 171
2: RESIDUES SER 15, SER 219, AND SER 247, SHOWED TWOFOLD DISORDERED POSITIONS FOR ATOM OG, HENCE THEIR ALTERNATE INDICATORS ARE *A* AND *B*. THEY HAVE AN OCCUPANCY OF 0.5 EACH, AND WERE REFINED AS DESCRIBED ABOVE.
3: ONE WATER (HOH 322) WAS LOCATED PRECISELY ON AN ELEMENT OF SYMMETRY, THEREFORE, IT WAS GIVEN HALF THE OCCUPANCY IT WOULD HAVE HAD, IF NOT LOCATED ON THE AXIS (OCC.=0.35).
4: ALL ATOMS OF THE PEPTIDE SEQUENCE WERE LOCATED, EXCEPT FOR THE SIDE-CHAIN OF THE C-TERMINAL GLN (278), WHICH WAS ONLY FOUND UP TO CB.
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

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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, peptidase K
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE THREE BENDS IN THIS STRUCTURE. S1: SER 79, GLY 83; S2: TRP 212, SER 216 (NESTED WITH T16); ...THERE ARE THREE BENDS IN THIS STRUCTURE. S1: SER 79, GLY 83; S2: TRP 212, SER 216 (NESTED WITH T16); S3: THR 244, ALA 248.
Sequence detailsTHE PROTEIN SEQUENCE (279 AMINO ACIDS) IS THE SAME AS THAT OF THE NATIVE ENZYME PRESENTED IN ...THE PROTEIN SEQUENCE (279 AMINO ACIDS) IS THE SAME AS THAT OF THE NATIVE ENZYME PRESENTED IN PROTEIN DATA BANK ENTRY 2PRK.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 %(w/v)protein1drop
250 mMTris-HCl1drop
3300 mMsodium-EDTA1drop
40.02 %1dropNaN3
50.75 M1reservoirNaNO3

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. obs: 33854 / % possible obs: 78 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.147

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.201 / Highest resolution: 1.5 Å
Details: THE OCCUPANCIES OF WATER OXYGENS COULD BE REFINED IN A LAST CYCLE OF REFINEMENT, BUT ONLY THOSE WITH OCCUPANCY GREATER THAN 0.5 WERE RETAINED.
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 1 194 2224
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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