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- PDB-6svi: Non-terahertz irradiated structure of bovine trypsin (even frames... -

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Basic information

Entry
Database: PDB / ID: 6svi
TitleNon-terahertz irradiated structure of bovine trypsin (even frames of crystal x42)
ComponentsCationic trypsin
KeywordsHYDROLASE / bovine trypsin / Terahertz irradiation / even frames / x42
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsAhlberg Gagner, V. / Lundholm, I. / Garcia-Bonete, M.J. / Rodilla, H. / Friedman, R. / Zhaunerchyk, V. / Bourenkov, G. / Schneider, T. / Stake, J. / Katona, G.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: Sci Rep / Year: 2019
Title: Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.
Authors: Gagner, V.A. / Lundholm, I. / Garcia-Bonete, M.J. / Rodilla, H. / Friedman, R. / Zhaunerchyk, V. / Bourenkov, G. / Schneider, T. / Stake, J. / Katona, G.
History
DepositionSep 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6775
Polymers23,3241
Non-polymers3524
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. ...Evidence: COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-30 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.910, 57.150, 65.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution - 60 mg/ml trypsin, 6 mg/ml benzamidine and 3 mM CaCl2 in a 30 mM HEPES buffer pH 7.0. Well solution - 18% PEG 8000, 200 mM (NH4)2SO4, 50 mM HEPES pH 7, 3 mM CaCl2 and 6 ...Details: protein solution - 60 mg/ml trypsin, 6 mg/ml benzamidine and 3 mM CaCl2 in a 30 mM HEPES buffer pH 7.0. Well solution - 18% PEG 8000, 200 mM (NH4)2SO4, 50 mM HEPES pH 7, 3 mM CaCl2 and 6 mg/ml benzamidine. 1:1 ratio drops

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.16→43.12 Å / Num. obs: 129363 / % possible obs: 94.6 % / Redundancy: 3.563 % / Biso Wilson estimate: 13.489 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.119 / Χ2: 1.233 / Net I/σ(I): 7.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.16-1.191.6580.7780.8343740.3261.0243.1
1.19-1.222.5460.7121.2990470.4570.87991.7
1.22-1.263.1850.6361.7894660.5810.76198.9
1.26-1.293.6370.5512.3293210.7110.64799.4
1.29-1.343.7910.4762.9189220.7750.55599.6
1.34-1.383.8040.4073.4887610.8430.47499.5
1.38-1.443.8150.354.283470.8690.40899.5
1.44-1.493.8140.2885.1680730.9130.33599.6
1.49-1.563.8250.2516.177360.9350.29299.7
1.56-1.643.8260.2087.3474590.9510.24299.7
1.64-1.733.7930.1788.5369830.9640.20799.4
1.73-1.833.8530.14510.2366490.9730.16999.2
1.83-1.963.8650.11512.7761880.9830.13399.2
1.96-2.113.7770.09114.9358080.9880.10699.1
2.11-2.313.7330.07816.5153270.9920.09199.1
2.31-2.593.5780.06717.7648190.9920.07998.7
2.59-2.993.3570.05918.6242040.9940.0798.2
2.99-3.663.7350.04922.7335870.9960.05798.9
3.66-5.183.7990.04125.1527740.9970.04899.5
5.18-43.123.6570.04224.6315180.9980.04999.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 418G

418g


Resolution: 1.16→43.12 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.19273 --
Rwork0.15061 --
obs-66493 95.97 %
Displacement parametersBiso mean: 13.035 Å2
Refinement stepCycle: LAST / Resolution: 1.16→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 20 288 1937

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