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- PDB-3l1k: SAD structure solution of proteinase K grown in potassium tellura... -

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Basic information

Entry
Database: PDB / ID: 3l1k
TitleSAD structure solution of proteinase K grown in potassium tellurate solution
ComponentsProteinase K
KeywordsHYDROLASE / ortho- meta- tellurate / Metal-binding / Serine protease / Zymogen
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
Orthotelluric acid / Proteinase K
Similarity search - Component
Biological speciesTritirachium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsJakoncic, J.
CitationJournal: To be Published
Title: SAD structure solution of proteinase K grown in potassium tellurate solution
Authors: Jakoncic, J.
History
DepositionDec 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,5457
Polymers28,9591
Non-polymers5866
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.902, 67.902, 102.181
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-447-

HOH

21A-699-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 genetically manipulated source
Source: (gene. exp.) Tritirachium album (fungus) / Gene: PROK / References: UniProt: P06873, peptidase K

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Non-polymers , 5 types, 429 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TE6 / Orthotelluric acid


Mass: 229.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H6O6Te
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUE 207 IS UNAMBIGUOUSLY IDENTIFIED AS ASP FROM THE ELECTRON DENSITY MAP EVEN THOUGH THE ...RESIDUE 207 IS UNAMBIGUOUSLY IDENTIFIED AS ASP FROM THE ELECTRON DENSITY MAP EVEN THOUGH THE CORRESPONDING UNP DATABASE CONTAINS SER. NO ENGINEERED MUTATIONS AT THIS POSITION HAVE BEEN INTRODUCED

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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: 39.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Drop was 1 microL of protein solution (80 mg/mL in dH2O) and 1 microL of well solution (1 mL of saturated solution of K2TeO4. The cryo-solution consisted of 70% of the crystallization ...Details: Drop was 1 microL of protein solution (80 mg/mL in dH2O) and 1 microL of well solution (1 mL of saturated solution of K2TeO4. The cryo-solution consisted of 70% of the crystallization solution and 30% of ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2007 / Details: Rh coated toroidal focusing mirror.
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 340169 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 40
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9.7 / Num. unique all: 9880 / % possible all: 67.9

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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: 1.55→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.92 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.14875 1751 5 %RANDOM
Rwork0.12289 ---
obs0.12415 33105 99.98 %-
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: 9.527 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 25 423 2479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212186
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.9442990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27523.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84615328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3841514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211696
X-RAY DIFFRACTIONr_mcbond_it0.791.51425
X-RAY DIFFRACTIONr_mcangle_it1.18522282
X-RAY DIFFRACTIONr_scbond_it1.9793761
X-RAY DIFFRACTIONr_scangle_it2.9094.5693
X-RAY DIFFRACTIONr_rigid_bond_restr1.01732186
X-RAY DIFFRACTIONr_sphericity_free3.8373435
X-RAY DIFFRACTIONr_sphericity_bonded1.75532134
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 96 -
Rwork0.216 2057 -
obs--100 %

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