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- PDB-3q5g: Sulphur SAD structure solution of proteinase K grown in SO4 solution -

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Basic information

Entry
Database: PDB / ID: 3q5g
TitleSulphur SAD structure solution of proteinase K grown in SO4 solution
ComponentsProteinase K
KeywordsHYDROLASE
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 / SAD / Resolution: 1.77 Å
AuthorsJakoncic, J.
CitationJournal: To be Published
Title: Crystallization of Macromolecules in Selenate to Solve the Phase Problem
Authors: Jakoncic, J.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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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)29,1874
Polymers28,9591
Non-polymers2283
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)67.864, 67.864, 102.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFROM THE ELECTRON DENSITY MAP RESIDUE 207 IS UNAMBIGUOUSLY IDENTIFIED AS ASP

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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: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 muL of 40 mg/ml protein mixed with 1 muL of the mother liquor. Mother liquor : 400 mM Ammonium SO4, 25 % glycerol, 100 mM Na cacodylate 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: 1.7712 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2010
Details: Si(111) channel cut mono. Rh coated toroidal focusing mirror.
RadiationMonochromator: 1.77 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. all: 24015 / Num. obs: 24015 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 25.4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 90.9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 16.6 / Num. unique all: 1175 / % possible all: 100

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Processing

Software
NameVersionClassification
DCS_X6Adata collection
SHELXSphasing
REFMAC5.5.0101refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.589 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16658 1226 5.1 %RANDOM
Rwork0.12383 ---
obs0.12596 22730 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: 10.457 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.124 Å
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 12 397 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212146
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9472932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01823.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69815318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9331512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211662
X-RAY DIFFRACTIONr_mcbond_it0.7131.51407
X-RAY DIFFRACTIONr_mcangle_it1.21722251
X-RAY DIFFRACTIONr_scbond_it2.2813739
X-RAY DIFFRACTIONr_scangle_it3.6944.5669
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 91 -
Rwork0.22 1632 -
obs--100 %

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