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- PDB-4wob: Proteinase-K Pre-Surface Acoustic Wave -

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Basic information

Entry
Database: PDB / ID: 4wob
TitleProteinase-K Pre-Surface Acoustic Wave
ComponentsProteinase K
KeywordsHYDROLASE / Surface Acoustic Wave / Nanocrystals / Crystal manipulation / Serial Crystallography / Acoustic Tweezers
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
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsFrench, J.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2OD007209-01 United States
National Science Foundation (NSF, United States)CBET-1438126 and IIP-1346440 United States
CitationJournal: Small / Year: 2015
Title: Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.
Authors: Guo, F. / Zhou, W. / Li, P. / Mao, Z. / Yennawar, N.H. / French, J.B. / Huang, T.J.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.0Jul 25, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / refine_hist / struct_ref
Item: _atom_site.occupancy / _entity_src_gen.gene_src_common_name ..._atom_site.occupancy / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ref.db_code
Revision 2.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,0552
Polymers28,9591
Non-polymers961
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.840, 67.840, 106.721
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-423-

HOH

21A-504-

HOH

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Components

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


Mass: 28958.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Tritirachium (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.6 - 1.6 M Ammonium Sulfate, 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18606 / % possible obs: 91 % / Redundancy: 6.6 % / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.9→31.505 Å / FOM work R set: 0.7735 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1849 10.01 %
Rwork0.1881 16625 -
obs0.195 18474 90.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.23 Å2 / Biso mean: 18.34 Å2 / Biso min: 7.54 Å2
Refinement stepCycle: final / Resolution: 1.9→31.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 5 296 2318
Biso mean--21.83 25.87 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062061
X-RAY DIFFRACTIONf_angle_d0.9872799
X-RAY DIFFRACTIONf_chiral_restr0.039312
X-RAY DIFFRACTIONf_plane_restr0.004368
X-RAY DIFFRACTIONf_dihedral_angle_d12.247709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8974-1.94870.34961220.27191098122079
1.9487-2.00610.32231250.25361125125082
2.0061-2.07080.3241300.2261176130686
2.0708-2.14480.34381390.23611244138390
2.1448-2.23070.28871420.22831268141092
2.2307-2.33210.34031420.22621285142791
2.3321-2.45510.28381460.20551307145394
2.4551-2.60880.30271470.2131307145493
2.6088-2.81010.26851460.1961321146794
2.8101-3.09270.28481440.18951300144492
3.0927-3.53970.22811440.16251299144392
3.5397-4.45760.19641510.14141358150993
4.4576-31.50930.19091710.15751537170899

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