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- PDB-5uvl: Serial Millisecond Crystallography of Membrane and Soluble Protei... -

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Basic information

Entry
Database: PDB / ID: 5uvl
TitleSerial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation
ComponentsProteinase K
KeywordsHYDROLASE
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 speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMartin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. ...Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketawala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
Funding support United States, 8items
OrganizationGrant numberCountry
Flinn Foundation1991 United States
STC Program of the National Science Foundation through BioXFEL1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM094618 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Y1-CO-1020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Y1-GM-1104 United States
Department of Energy (DOE, United States)DE-AC02-06CH1135 United States
CitationJournal: IUCrJ / Year: 2017
Title: Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.
Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / ...Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketwala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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.year
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,1635
Polymers28,9591
Non-polymers2044
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.300, 68.300, 108.200
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 / / 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: unidentified (others) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.01 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.5 M sodium nitrate, 0.1 M calcium chloride

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.65→50.01 Å / Num. obs: 6769 / % possible obs: 99.2 % / Redundancy: 104.8 % / Net I/σ(I): 4.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
Cootmodel building
MOLREPphasing
Cheetahdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AVJ

5avj


Resolution: 2.65→50.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 24.593 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24269 1095 13.9 %RANDOM
Rwork0.22541 ---
obs0.22789 6769 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2--0.18 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.65→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 10 0 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192078
X-RAY DIFFRACTIONr_bond_other_d0.0020.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9372822
X-RAY DIFFRACTIONr_angle_other_deg0.94134276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31423.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35615299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8431512
X-RAY DIFFRACTIONr_chiral_restr0.060.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022461
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
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_it3.1555.8641115
X-RAY DIFFRACTIONr_mcbond_other3.1465.8641114
X-RAY DIFFRACTIONr_mcangle_it4.798.7981392
X-RAY DIFFRACTIONr_mcangle_other4.7928.7991393
X-RAY DIFFRACTIONr_scbond_it3.9666.351963
X-RAY DIFFRACTIONr_scbond_other3.876.324958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0429.3351425
X-RAY DIFFRACTIONr_long_range_B_refined9.8357.0219576
X-RAY DIFFRACTIONr_long_range_B_other9.8357.0239577
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 63 -
Rwork0.41 460 -
obs--91.27 %

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