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- PDB-5cw1: Proteinase K complexed with 4-iodopyrazole -

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Basic information

Entry
Database: PDB / ID: 5cw1
TitleProteinase K complexed with 4-iodopyrazole
ComponentsProteinase K
KeywordsHYDROLASE / 4-iodopyrazole / phasing / proteinase K / fragment screening
Function / homology
Function and homology information


peptidase K / cellular anatomical entity / serine-type endopeptidase activity / proteolysis / 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
IODIDE ION / 4-IODOPYRAZOLE / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.45 Å
AuthorsBauman, J.D. / Arnold, E.
CitationJournal: Iucrj / Year: 2016
Title: Rapid experimental SAD phasing and hot spot identification with halogenated fragments
Authors: Bauman, J.D. / Harrison, J.J.E.K. / Arnold, E.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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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)29,9878
Polymers28,9591
Non-polymers1,0287
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.017, 68.017, 102.045
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-307-

IOD

21A-549-

HOH

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Components

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


Mass: 28958.791 Da / Num. of mol.: 1 / Fragment: UNP residues 106-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Engyodontium album (fungus) / Gene: PROK / Production host: Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H3IN2
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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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: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 100mM Tris pH7.2 and 1.28 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→35 Å / Num. obs: 42913 / % possible obs: 99.45 % / Redundancy: 12.8 % / Net I/σ(I): 55.7

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Processing

Software
NameVersionClassification
PHENIXdev_1988refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→34.998 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1531 2156 5.02 %
Rwork0.1308 --
obs0.1319 42912 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→34.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 30 397 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082111
X-RAY DIFFRACTIONf_angle_d1.1712882
X-RAY DIFFRACTIONf_dihedral_angle_d11.882732
X-RAY DIFFRACTIONf_chiral_restr0.072321
X-RAY DIFFRACTIONf_plane_restr0.007377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48380.33541170.30632467X-RAY DIFFRACTION92
1.4838-1.52090.17471510.15892679X-RAY DIFFRACTION100
1.5209-1.5620.12681420.10642670X-RAY DIFFRACTION100
1.562-1.6080.16031370.11542704X-RAY DIFFRACTION100
1.608-1.65990.16831420.1222704X-RAY DIFFRACTION100
1.6599-1.71920.1551420.10892685X-RAY DIFFRACTION100
1.7192-1.7880.13261440.10522707X-RAY DIFFRACTION100
1.788-1.86940.12121510.10572698X-RAY DIFFRACTION100
1.8694-1.96790.13271470.10512693X-RAY DIFFRACTION100
1.9679-2.09120.14041490.10582727X-RAY DIFFRACTION100
2.0912-2.25270.13521590.11462712X-RAY DIFFRACTION100
2.2527-2.47930.13991510.11482744X-RAY DIFFRACTION100
2.4793-2.83790.14931560.12512765X-RAY DIFFRACTION100
2.8379-3.57490.14641250.13832821X-RAY DIFFRACTION100
3.5749-35.00780.19431430.17342980X-RAY DIFFRACTION100

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