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- PDB-4dj5: Proteinase K by Langmuir-Blodgett Hanging Drop Method at 1.8A res... -

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Basic information

Entry
Database: PDB / ID: 4dj5
TitleProteinase K by Langmuir-Blodgett Hanging Drop Method at 1.8A resolution for Unique Water Distribution
ComponentsProteinase K
KeywordsHYDROLASE / Thin Film / Langmuir Blodgett
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsPechkova, E. / Sivozhelezov, V. / Belmonte, L. / Nicolini, C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Unique water distribution of Langmuir-Blodgett versus classical crystals.
Authors: Pechkova, E. / Sivozhelezov, V. / Belmonte, L. / Nicolini, C.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Proteinase K


Theoretical massNumber of molelcules
Total (without water)28,9311
Polymers28,9311
Non-polymers00
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.950, 67.950, 102.180
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
11X-377-

HOH

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Components

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


Mass: 28930.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Engyodontium album (fungus) / Gene: PROK / References: UniProt: P06873, peptidase K
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 39.66 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97633 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.8→56.581 Å / Num. all: 22770 / Num. obs: 22770 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rsym value: 0.096 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.96.70.1085.12185632830.108100
1.9-2.016.80.1134.92100531020.113100
2.01-2.156.60.115.11941329220.11100
2.15-2.326.60.1015.21789727210.10199.9
2.32-2.556.30.0915.91595025330.091100
2.55-2.856.30.095.81419022540.0998.5
2.85-3.297.20.0915.71466620430.09199.9
3.29-4.036.90.0915.91206417580.09199.7
4.03-5.696.60.0896.1913813750.08998.9
5.69-24.0545.90.0925.746167790.09294.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å24.06 Å
Translation1.85 Å24.06 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.05 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2537 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.881 / SU B: 2.247 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1329 / SU Rfree: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1166 5.1 %RANDOM
Rwork0.1563 ---
obs0.1587 22707 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.19 Å2 / Biso mean: 7.808 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 455 2485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212071
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9372816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55523.61483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05515299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3081512
X-RAY DIFFRACTIONr_chiral_restr0.1460.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211602
X-RAY DIFFRACTIONr_mcbond_it0.831.51371
X-RAY DIFFRACTIONr_mcangle_it1.67122178
X-RAY DIFFRACTIONr_scbond_it3.5863700
X-RAY DIFFRACTIONr_scangle_it5.3534.5638
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 100 -
Rwork0.143 1553 -
all-1653 -
obs--99.76 %

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