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- PDB-3qmp: Selenium SAD structure solution of proteinase K grown in SO4-less... -

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Basic information

Entry
Database: PDB / ID: 3qmp
TitleSelenium SAD structure solution of proteinase K grown in SO4-less solution and soaked in selenate.
ComponentsProteinase K
KeywordsHYDROLASE
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/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
SELENATE ION / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsJakoncic, J.
CitationJournal: To be Published
Title: Crystallization of macromolecules in selenate to solve the phase problem
Authors: Jakoncic, J.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release

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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)29,3547
Polymers28,9591
Non-polymers3956
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.967, 67.967, 102.215
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-460-

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.) Engyodontium album (fungus) / Gene: PROK / References: UniProt: P06873, peptidase K
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SE4 / SELENATE ION


Mass: 142.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O4Se
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: UL OF 40 MG/ML PROTEIN AND 1 UL OF WELL SOLUTION: 10 MM CACL2, 500 MM NANO3, 100 MM NA CACODYLATE. Crystal soaked in 33 % (V/V) glycerol, 0.33 M NaSeO4 and 33 % (V/V) mother liquor., pH 6.5, ...Details: UL OF 40 MG/ML PROTEIN AND 1 UL OF WELL SOLUTION: 10 MM CACL2, 500 MM NANO3, 100 MM NA CACODYLATE. Crystal soaked in 33 % (V/V) glycerol, 0.33 M NaSeO4 and 33 % (V/V) mother liquor., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2010
Details: SI(111) CHANNEL CUT MONO AND RH COATED TORROIDAL FOCUSING MIRROR.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. all: 97410 / Num. obs: 97410 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15 % / Biso Wilson estimate: 4.3 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 32.8
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 6.5 / Num. unique all: 4800 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DCS_X6Adata collection
SHELXSphasing
REFMAC5.5.0087refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.1→19.81 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.547 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11867 4865 5 %RANDOM
Rwork0.10272 ---
obs0.10352 92347 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 4.975 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.022 Å
Refinement stepCycle: LAST / Resolution: 1.1→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 15 458 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212298
X-RAY DIFFRACTIONr_bond_other_d0.0010.021520
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9483173
X-RAY DIFFRACTIONr_angle_other_deg0.89333737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90523.67398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44315355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4221516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
X-RAY DIFFRACTIONr_mcbond_it0.8421.51483
X-RAY DIFFRACTIONr_mcbond_other0.3381.5618
X-RAY DIFFRACTIONr_mcangle_it1.29122402
X-RAY DIFFRACTIONr_scbond_it1.8463815
X-RAY DIFFRACTIONr_scangle_it2.7294.5740
X-RAY DIFFRACTIONr_rigid_bond_restr0.72833818
X-RAY DIFFRACTIONr_sphericity_free4.3633532
X-RAY DIFFRACTIONr_sphericity_bonded1.933744
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 336 -
Rwork0.139 6714 -
obs--100 %

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