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- PDB-1p7w: Crystal structure of the complex of Proteinase K with a designed ... -

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Basic information

Entry
Database: PDB / ID: 1p7w
TitleCrystal structure of the complex of Proteinase K with a designed heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ser-Ala at atomic resolution
Components
  • inhibitor peptide
  • proteinase K
KeywordsHYDROLASE / Proteinase K / atomic resolution / inhibitor peptide
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsBilgrami, S. / Perbandt, M. / Chandra, V. / Banumathi, S. / Kaur, P. / Betzel, C. / Singh, T.P.
CitationJournal: To be published
Title: Crystal structure of the complex of Proteinase K with heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ser-Ala at atomic resolution
Authors: Bilgrami, S. / Perbandt, M. / Chandra, V. / Banumathi, S. / Kaur, P. / Betzel, C. / Singh, T.P.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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_conn.ptnr2_label_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: proteinase K
B: inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0099
Polymers29,6192
Non-polymers3907
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-23 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.835, 67.835, 101.563
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 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Protein/peptide inhibitor peptide


Mass: 659.730 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


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


Mass: 18.015 Da / Num. of mol.: 432 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 295 K / Method: microgravity with APCF reactors / pH: 6.5
Details: Tris HCl, CaCl2, NaNO3, pH 6.5, microgravity with APCF reactors, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.02→20 Å / Num. all: 119205 / Num. obs: 119205 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 15.8 % / Biso Wilson estimate: 5 Å2 / Rsym value: 0.063 / Net I/σ(I): 24.4
Reflection shellResolution: 1.02→1.06 Å / Mean I/σ(I) obs: 5.58 / Num. unique all: 11282 / Rsym value: 0.234 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IC6

1ic6


Resolution: 1.02→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.235 / SU ML: 0.013 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14162 1192 1 %RANDOM
Rwork0.12904 ---
all0.12917 119205 --
obs0.1291 119205 99.82 %-
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: 7.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 22 432 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212141
X-RAY DIFFRACTIONr_bond_other_d0.0060.021821
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9432903
X-RAY DIFFRACTIONr_angle_other_deg0.91934233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165284
X-RAY DIFFRACTIONr_chiral_restr0.2180.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022487
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02443
X-RAY DIFFRACTIONr_nbd_refined0.2630.2554
X-RAY DIFFRACTIONr_nbd_other0.2760.22388
X-RAY DIFFRACTIONr_nbtor_other0.0880.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5430.285
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4120.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4090.2115
X-RAY DIFFRACTIONr_mcbond_it1.0661.51427
X-RAY DIFFRACTIONr_mcangle_it1.70422231
X-RAY DIFFRACTIONr_scbond_it2.4863714
X-RAY DIFFRACTIONr_scangle_it3.7364.5672
X-RAY DIFFRACTIONr_rigid_bond_restr1.09522141
X-RAY DIFFRACTIONr_sphericity_free6.9672455
X-RAY DIFFRACTIONr_sphericity_bonded2.46122105
LS refinement shellResolution: 1.02→1.045 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 91
Rwork0.182 8138

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