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- PDB-4zar: Crystal Structure of Proteinase K from Engyodontium albuminhibite... -

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Entry
Database: PDB / ID: 4zar
TitleCrystal Structure of Proteinase K from Engyodontium albuminhibited by METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE at 1.15 A resolution
Components
  • METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE, bound form
  • Proteinase K
Keywordshydrolase/hydrolase inhibitor / Serine Protease inhibitor / hydrolase-hydrolase inhibitor complex
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/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
METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsSawaya, M.R. / Cascio, D. / Collazo, M. / Bond, C. / Cohen, A. / DeNicola, A. / Eden, K. / Jain, K. / Leung, C. / Lubock, N. ...Sawaya, M.R. / Cascio, D. / Collazo, M. / Bond, C. / Cohen, A. / DeNicola, A. / Eden, K. / Jain, K. / Leung, C. / Lubock, N. / McCormick, J. / Rosinski, J. / Spiegelman, L. / Athar, Y. / Tibrewal, N. / Winter, J. / Solomon, S.
Citation
Journal: to be published
Title: Crystal Structure of Proteinase K from Engyodontium album inhibited by METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE at 1.15 A resolution
Authors: Sawaya, M.R. / Cascio, D. / Collazo, M. / Bond, C. / Cohen, A. / DeNicola, A. / Eden, K. / Jain, K. / Leung, C. / Lubock, N. / McCormick, J. / Rosinski, J. / Spiegelman, L. / Athar, Y. / ...Authors: Sawaya, M.R. / Cascio, D. / Collazo, M. / Bond, C. / Cohen, A. / DeNicola, A. / Eden, K. / Jain, K. / Leung, C. / Lubock, N. / McCormick, J. / Rosinski, J. / Spiegelman, L. / Athar, Y. / Tibrewal, N. / Winter, J. / Solomon, S.
#1: Journal: J. Biol. Chem. / Year: 1991
Title: Inhibition of proteinase K by methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone. An x-ray study at 2.2-A resolution.
Authors: Wolf, W.M. / Bajorath, J. / Mueller, A. / Raghunathan, S. / Singh, T.P. / Hinrichs, W. / Saenger, W.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / pdbx_database_related ...entity / pdbx_database_related / pdbx_entity_src_syn / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _entity.src_method / _pdbx_database_related.content_type ..._entity.src_method / _pdbx_database_related.content_type / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
B: METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE, bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5904
Polymers29,5102
Non-polymers802
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-26 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.850, 67.850, 102.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

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Components

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


Mass: 28958.791 Da / Num. of mol.: 1 / Fragment: unp residues 106-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Engyodontium album (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P06873, peptidase K
#2: Protein/peptide METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE, bound form


Type: Peptide-like / Class: Inhibitor / Mass: 551.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 37.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium Sulfate , Tris HCL, calcium chloride / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.15→56.6 Å / Num. obs: 82922 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 16.018 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Χ2: 1 / Net I/σ(I): 18.82 / Num. measured all: 1014404
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.15-1.180.8590.5913.2637346620846190.6374.4
1.18-1.210.9080.5154.1850966608853230.54487.4
1.21-1.250.9510.4655.4169373587058530.48699.7
1.25-1.290.9640.4286.3473556575557480.44699.9
1.29-1.330.9730.3467.5270234556755670.361100
1.33-1.370.9760.2918.5764937538953890.304100
1.37-1.430.9870.24210.4968519520352020.252100
1.43-1.480.9910.19712.8365474502350230.206100
1.48-1.550.9940.15415.761161484148360.16199.9
1.55-1.630.9950.12418.4456858460946030.12999.9
1.63-1.710.9960.10622.5859420442544250.11100
1.71-1.820.9970.08926.0654898415841580.093100
1.82-1.940.9970.07530.449441394039390.078100
1.94-2.10.9980.06535.3746414368336760.06799.8
2.1-2.30.9980.0639.845231340334030.063100
2.3-2.570.9980.05641.7440445310131010.058100
2.57-2.970.9990.05142.332715273927250.05499.5
2.97-3.640.9990.0547.2731309236123610.052100
3.64-5.140.9980.04746.7822994186918660.04999.8
5.140.9980.04445.7213113110911050.04699.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PRK

3prk


Resolution: 1.15→56.58 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.84 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1345 8293 10 %RANDOM
Rwork0.1099 ---
obs0.1124 74629 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.91 Å2 / Biso mean: 14.417 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.15→56.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 2 318 2386
Biso mean--14.33 27.61 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192228
X-RAY DIFFRACTIONr_bond_other_d0.0010.022011
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9413056
X-RAY DIFFRACTIONr_angle_other_deg0.934642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5255.032316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2823.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5091515
X-RAY DIFFRACTIONr_chiral_restr0.1180.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_mcbond_it1.3221.1761169
X-RAY DIFFRACTIONr_mcbond_other1.3231.1761168
X-RAY DIFFRACTIONr_mcangle_it1.3761.7721468
X-RAY DIFFRACTIONr_rigid_bond_restr4.25734239
X-RAY DIFFRACTIONr_sphericity_free25.404569
X-RAY DIFFRACTIONr_sphericity_bonded8.84354425
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 462 -
Rwork0.168 4156 -
all-4618 -
obs--74.4 %

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