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- PDB-5whw: Using sound pulses to solve the crystal harvesting bottleneck -

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Basic information

Entry
Database: PDB / ID: 5whw
TitleUsing sound pulses to solve the crystal harvesting bottleneck
ComponentsProteinase K
KeywordsHYDROLASE / Crystal harvesting / drug discovery / acoustic droplet ejection
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / membrane
Similarity search - Function
: / VtrA C-terminal periplasmic domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Peptidase S8/S53 domain / Subtilase family / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily ...: / VtrA C-terminal periplasmic domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Peptidase S8/S53 domain / Subtilase family / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Putative transcriptional regulator ToxR
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsSoares, A.S. / Brennan, H.M. / Natarajan, R. / McCarthy, L. / Leroy, L.
Funding support United States, Brazil, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
Department of Energy (DOE, United States)KP1605010 United States
CAPES17040/12-4 Brazil
Workforce Development for Teachers and Scientists (WDTS) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DMR-0936384 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Using sound pulses to solve the crystal-harvesting bottleneck.
Authors: Samara, Y.N. / Brennan, H.M. / McCarthy, L. / Bollard, M.T. / Laspina, D. / Wlodek, J.M. / Campos, S.L. / Natarajan, R. / Gofron, K. / McSweeney, S. / Soares, A.S. / Leroy, L.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4508
Polymers28,9591
Non-polymers4927
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.719, 67.719, 107.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-736-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28958.791 Da / Num. of mol.: 1 / Fragment: residues 106-384 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K

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Non-polymers , 5 types, 434 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M sodium nitrate, 0.16 M calcium chloride, 0.2 M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97908 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.71→57.27 Å / Num. obs: 26111 / % possible obs: 99.75 % / Redundancy: 12.9 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fon

5fon


Resolution: 1.71→57.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.784 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17332 1356 4.9 %RANDOM
Rwork0.15158 ---
obs0.15268 26111 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.469 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.71→57.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 29 427 2488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192220
X-RAY DIFFRACTIONr_bond_other_d0.0020.021992
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9423035
X-RAY DIFFRACTIONr_angle_other_deg1.0134597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5515314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83623.93694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87315326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.621514
X-RAY DIFFRACTIONr_chiral_restr0.1320.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02534
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.2511172
X-RAY DIFFRACTIONr_mcbond_other1.241.251171
X-RAY DIFFRACTIONr_mcangle_it1.6631.8761481
X-RAY DIFFRACTIONr_mcangle_other1.6641.8781482
X-RAY DIFFRACTIONr_scbond_it2.2841.5031048
X-RAY DIFFRACTIONr_scbond_other2.2831.5031048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3032.1631544
X-RAY DIFFRACTIONr_long_range_B_refined6.58112.9292894
X-RAY DIFFRACTIONr_long_range_B_other5.53311.4062666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.714→1.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 89 -
Rwork0.349 1832 -
obs--97.02 %

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