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- PDB-2v8b: SAD Structure solution of Proteinase K grown in selenate solution -

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Basic information

Entry
Database: PDB / ID: 2v8b
TitleSAD Structure solution of Proteinase K grown in selenate solution
ComponentsPROTEINASE K
KeywordsHYDROLASE / EXPERIMENTAL PHASING / METAL-BINDING / SERINE PROTEASE / SULFATE / ZYMOGEN / PROTEASE
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/S53 domain / : / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / 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: 0.94 Å
AuthorsJakoncic, J. / Stojanoff, V.
CitationJournal: To be Published
Title: Selenate Substitution: Application in Protein Crystallography
Authors: Jakoncic, J. / Stojanoff, V.
History
DepositionAug 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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)29,1423
Polymers28,9591
Non-polymers1832
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.053, 68.053, 102.553
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-2266-

HOH

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Components

#1: Protein PROTEINASE K / TRITIRACHIUM ALKALINE PROTEINASE / ENDOPEPTIDASE K


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SE4 / SELENATE ION


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


Mass: 18.015 Da / Num. of mol.: 538 / 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 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HANGING DROP AT 20C, 50 TO 200 MM NASEO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8551
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 27, 2007 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8551 Å / Relative weight: 1
ReflectionResolution: 0.95→20 Å / Num. obs: 1875402 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.5
Reflection shellResolution: 0.94→0.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 0.94→20 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.259 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.103 7746 5 %RANDOM
Rwork0.09 ---
obs0.091 146726 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 4.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 0.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 6 538 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212295
X-RAY DIFFRACTIONr_bond_other_d0.0020.021508
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9483175
X-RAY DIFFRACTIONr_angle_other_deg0.98733727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91223.89595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69815361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3681514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02486
X-RAY DIFFRACTIONr_nbd_refined0.2470.2467
X-RAY DIFFRACTIONr_nbd_other0.1970.21733
X-RAY DIFFRACTIONr_nbtor_refined0.180.21188
X-RAY DIFFRACTIONr_nbtor_other0.0920.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3341.51531
X-RAY DIFFRACTIONr_mcbond_other0.3981.5623
X-RAY DIFFRACTIONr_mcangle_it1.81122422
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8123878
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.774.5716
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.94→0.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 534 -
Rwork0.178 10280 -
obs--95.03 %

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