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- PDB-4woc: Proteinase-K Post-Surface Acoustic Waves -

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Basic information

Entry
Database: PDB / ID: 4woc
TitleProteinase-K Post-Surface Acoustic Waves
ComponentsProteinase K
KeywordsHYDROLASE / Surface Acoustic Waves / Crystal Manipulation / Serial Crystallography / Acoustic Tweezers / Nanocrystals
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
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.601 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
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
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_oper_list.symmetry_operation
Revision 1.3Jul 25, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct_ref.db_code
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 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
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,1513
Polymers28,9591
Non-polymers1922
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-38 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.687, 67.687, 102.010
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-470-

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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.6 - 1.6 Ammonium Sulfate, 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 31109 / % possible obs: 97 % / Redundancy: 3.7 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.601→19.737 Å / FOM work R set: 0.8454 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 1995 6.46 %
Rwork0.1737 28890 -
obs0.1759 30885 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.09 Å2 / Biso mean: 14.79 Å2 / Biso min: 6.82 Å2
Refinement stepCycle: final / Resolution: 1.601→19.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 10 346 2383
Biso mean--24.34 24.69 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062076
X-RAY DIFFRACTIONf_angle_d1.0092820
X-RAY DIFFRACTIONf_chiral_restr0.041312
X-RAY DIFFRACTIONf_plane_restr0.005370
X-RAY DIFFRACTIONf_dihedral_angle_d11.522714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6014-1.64150.2361330.20721933206692
1.6415-1.68580.24641360.19871960209694
1.6858-1.73540.26361380.19411996213495
1.7354-1.79140.25321380.20232001213996
1.7914-1.85540.26431410.20512037217897
1.8554-1.92960.29681420.21852043218597
1.9296-2.01730.2111400.19332032217297
2.0173-2.12360.24231430.18042073221697
2.1236-2.25640.23691410.1922058219996
2.2564-2.43040.21151430.1652068221198
2.4304-2.67440.18281470.16942124227199
2.6744-3.06020.20011480.15692146229499
3.0602-3.85080.1511490.1462150229998
3.8508-19.73850.18741560.16422269242598

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