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- PDB-8f05: Proteinase K Anomalous Dataset at 293 K and 7.1 keV -

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Basic information

Entry
Database: PDB / ID: 8f05
TitleProteinase K Anomalous Dataset at 293 K and 7.1 keV
ComponentsProteinase K
KeywordsHYDROLASE / Proteinase K / serine proteases
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 speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDoukov, T. / Yabukarski, F. / Herschlag, D.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
Human Frontier Science Program (HFSP) France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.
Authors: Doukov, T. / Herschlag, D. / Yabukarski, F.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)29,6719
Polymers28,9591
Non-polymers7138
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-89 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.006, 68.006, 102.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

21A-610-

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 genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Parengyodontium album (fungus) / 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 uL 1 M ammonium sulfate + 2 uL 10 mg/mL proteinase K in 50 mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.7462 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7462 Å / Relative weight: 1
ReflectionResolution: 1.8→35.062 Å / Num. obs: 22708 / % possible obs: 98.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.018 / Net I/σ(I): 39.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 12.4 / Num. unique obs: 1140 / CC1/2: 0.992 / Rpim(I) all: 0.055 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.062 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.141 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1401 1148 5.067 %
Rwork0.1092 21507 -
all0.111 --
obs-22655 98.611 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.823 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å20 Å20 Å2
2---0.004 Å20 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 36 220 2288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122264
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161920
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.6433112
X-RAY DIFFRACTIONr_angle_other_deg0.5681.5574515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.373517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56710342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1021097
X-RAY DIFFRACTIONr_chiral_restr0.0770.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
X-RAY DIFFRACTIONr_nbd_refined0.220.2406
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21732
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2130
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.215
X-RAY DIFFRACTIONr_nbd_other0.1620.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.220
X-RAY DIFFRACTIONr_mcbond_it0.9941.111176
X-RAY DIFFRACTIONr_mcbond_other0.9811.111176
X-RAY DIFFRACTIONr_mcangle_it1.4082.0641482
X-RAY DIFFRACTIONr_mcangle_other1.4112.0711483
X-RAY DIFFRACTIONr_scbond_it3.561.7631088
X-RAY DIFFRACTIONr_scbond_other3.5251.7391061
X-RAY DIFFRACTIONr_scangle_it4.82.9911608
X-RAY DIFFRACTIONr_scangle_other4.7672.9431567
X-RAY DIFFRACTIONr_lrange_it6.20113.8492549
X-RAY DIFFRACTIONr_lrange_other6.04511.8462510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.214750.14213620.14516660.9820.99286.25450.13
1.847-1.8970.179740.11814670.12216130.9850.99395.53630.109
1.897-1.9520.149750.10915110.11115860.9870.9931000.102
1.952-2.0120.159800.10114320.10315150.9840.99499.8020.095
2.012-2.0780.125810.09514060.09714870.990.9941000.092
2.078-2.150.147650.09813640.114290.9870.9951000.096
2.15-2.2310.125650.113330.10114040.9920.99499.57260.099
2.231-2.3220.144680.10412700.10613380.9850.9941000.105
2.322-2.4240.15720.10312300.10513020.9860.9931000.105
2.424-2.5420.127570.10311780.10512350.9910.9931000.107
2.542-2.6790.118630.09911150.111780.9910.9941000.105
2.679-2.840.163650.10810680.11111330.9830.9931000.115
2.84-3.0350.169530.1210010.12210550.9830.99199.90520.133
3.035-3.2760.154560.1179460.11910020.9880.9921000.13
3.276-3.5860.12350.1098870.119220.990.9931000.126
3.586-4.0040.098440.0957970.0958410.9940.9951000.114
4.004-4.6130.08460.0897000.0887460.9960.9961000.109
4.613-5.6260.137320.0996230.16580.990.99599.54410.115
5.626-7.8560.146230.1534990.1535220.9850.9871000.184
7.856-35.0620.253190.213180.2133370.9730.971000.3
Refinement TLS params.Method: refined / Origin x: 51.8925 Å / Origin y: 12.9764 Å / Origin z: 0.2887 Å
111213212223313233
T0.0049 Å2-0.0007 Å2-0.0026 Å2-0.0012 Å2-0.0005 Å2--0.0031 Å2
L1.0096 °2-0.1018 °2-0.0228 °2-0.8818 °20.0847 °2--0.5741 °2
S0.0079 Å °0.0289 Å °-0.0284 Å °0.0058 Å °-0.0095 Å °0.0268 Å °0.0175 Å °0.0027 Å °0.0015 Å °
Refinement TLS groupSelection: ALL

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