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- PDB-7s4z: Serial Macromolecular Crystallography at ALBA Synchrotron Light S... -

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Basic information

Entry
Database: PDB / ID: 7s4z
TitleSerial Macromolecular Crystallography at ALBA Synchrotron Light Source - Proteinase K
ComponentsProteinase K
KeywordsHYDROLASE / Serial Crystallography / LCP Injection
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 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 ...Proteinase K-like catalytic 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
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMartin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. ...Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, R. / Carpena, X.
Funding support2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306
Other government2019-T1BMD-15552
CitationJournal: J.Synchrotron Radiat. / Year: 2022
Title: Serial macromolecular crystallography at ALBA Synchrotron Light Source.
Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / ...Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, D.R. / Carpena, X.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1014
Polymers28,9591
Non-polymers1423
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.400, 68.400, 108.400
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-448-

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: Escherichia coli (E. coli) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.1 M MES pH 6.5, 0.5 sodium citrate, 0.1 M calcium chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→48.4 Å / Num. obs: 21010 / % possible obs: 100 % / Redundancy: 3757 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.9985 / CC star: 0.9996 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 315 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2033 / CC1/2: 0.2255 / CC star: 0.6067 / % possible all: 100
Serial crystallography sample deliveryDescription: LCP Injection / Method: injection
Serial crystallography sample delivery injectionInjector diameter: 5.0E-5 µm
Serial crystallography data reductionFrames total: 577904 / Lattices indexed: 216645

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELv0.10.0data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IC6

1ic6


Resolution: 1.9→44.21 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.602 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19559 1071 5.1 %RANDOM
Rwork0.16508 ---
obs0.16664 19879 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 6 89 2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0172075
X-RAY DIFFRACTIONr_bond_other_d0.0010.0191854
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.842820
X-RAY DIFFRACTIONr_angle_other_deg1.1962.6644260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81221.97996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8041512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_mcbond_it0.9082.2581115
X-RAY DIFFRACTIONr_mcbond_other0.9072.2571114
X-RAY DIFFRACTIONr_mcangle_it1.343.3821392
X-RAY DIFFRACTIONr_mcangle_other1.3393.3831393
X-RAY DIFFRACTIONr_scbond_it1.6372.513960
X-RAY DIFFRACTIONr_scbond_other1.6352.504958
X-RAY DIFFRACTIONr_scangle_other2.6723.671426
X-RAY DIFFRACTIONr_long_range_B_refined3.95727.3942311
X-RAY DIFFRACTIONr_long_range_B_other3.95427.2652300
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.516 79 -
Rwork0.508 1431 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 16.555 Å / Origin y: -12.766 Å / Origin z: -0.178 Å
111213212223313233
T0.0245 Å2-0.0001 Å2-0.0003 Å2-0.0007 Å2-0.001 Å2--0.0349 Å2
L1.2474 °2-0.1246 °2-0.0731 °2-1.3194 °20.0828 °2--0.8574 °2
S-0.0062 Å °-0.0007 Å °0.0037 Å °0.0852 Å °0.0155 Å °-0.0375 Å °0.0338 Å °-0.0187 Å °-0.0094 Å °

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