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- PDB-2pq2: Structure of serine proteinase K complex with a highly flexible h... -

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Basic information

Entry
Database: PDB / ID: 2pq2
TitleStructure of serine proteinase K complex with a highly flexible hydrophobic peptide at 1.8A resolution
Components
  • GALAG peptide
  • Proteinase K
KeywordsHYDROLASE / PROTEINASE K / HYDROPHOBIC PEPTIDE GALAG / COMPLEX
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
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsEthayathulla, A.S. / Singh, A.K. / Singh, N. / Sharma, S. / Sinha, M. / Somvanshi, R.K. / Kaur, P. / Dey, S. / Srinivasan, A. / Singh, T.P.
CitationJournal: To be Published
Title: Structure of serine proteinase K complex with a highly flexible hydrophobic peptide at 1.8A resolution
Authors: Ethayathulla, A.S. / Singh, A.K. / Singh, N. / Sharma, S. / Sinha, M. / Somvanshi, R.K. / Kaur, P. / Dey, S. / Srinivasan, A. / Singh, T.P.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
B: GALAG peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4484
Polymers29,3462
Non-polymers1022
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.314, 68.314, 108.418
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 / / Tritirachium alkaline proteinase / Endopeptidase K


Mass: 28958.791 Da / Num. of mol.: 1 / Mutation: S312D / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / Strain: FUNGIFungus / References: UniProt: P06873, peptidase K
#2: Protein/peptide GALAG peptide


Mass: 387.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M AMMONIUM ACTATE, 0.1M SODIUM ACETATE, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2007 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→57.3 Å / Num. all: 24800 / Num. obs: 23699 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.0561 / Net I/σ(I): 12.2
Reflection shellResolution: 1.82→1.87 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.261 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DP4

2dp4


Resolution: 1.82→57.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.594 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20728 1216 5.1 %RANDOM
Rwork0.16823 ---
all0.17211 23699 --
obs0.17016 22483 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.82→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 5 263 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212124
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.942895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32823.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83215306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9151512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021650
X-RAY DIFFRACTIONr_nbd_refined0.3080.21050
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2184
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.217
X-RAY DIFFRACTIONr_mcbond_it0.6711.51437
X-RAY DIFFRACTIONr_mcangle_it1.14222243
X-RAY DIFFRACTIONr_scbond_it2.1043784
X-RAY DIFFRACTIONr_scangle_it3.2214.5646
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 91 -
Rwork0.276 1623 -
obs--100 %

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