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- PDB-6svv: Reference structure of bovine trypsin (odd frames of crystal x30) -

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Basic information

Entry
Database: PDB / ID: 6svv
TitleReference structure of bovine trypsin (odd frames of crystal x30)
ComponentsCationic trypsin
KeywordsHYDROLASE / bovine trypsin / Terahertz irradiation / odd frames / x30
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 19, 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 1.2Oct 23, 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-29 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.480, 56.760, 65.130
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 (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: 2.08 Å3/Da / Density % sol: 40.77 %
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: 1.15→42.83 Å / Num. obs: 126973 / % possible obs: 94 % / Redundancy: 3.34 % / Biso Wilson estimate: 14.914 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.109 / Χ2: 1.254 / Net I/σ(I): 7.43 / Num. measured all: 424102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.15-1.181.5030.7930.6655521009636950.3791.0536.6
1.18-1.222.3520.7740.9321016970289360.420.97592.1
1.22-1.252.970.6931.2927681941493200.5050.84199
1.25-1.293.4510.6261.7131729921591950.6190.74199.8
1.29-1.333.6120.5232.2132174892789070.7310.61499.8
1.33-1.383.6410.452.7131225860485770.7880.52799.7
1.38-1.433.6240.3853.2629951830382640.8330.45299.5
1.43-1.493.5830.2994.1828706803280110.90.35299.7
1.49-1.563.5580.2455.0927093764076150.9310.28899.7
1.56-1.633.5330.26.3725859735873190.9450.23699.5
1.63-1.723.50.177.6424428701669790.9620.20199.5
1.72-1.823.5450.1369.6523100655265170.9770.16199.5
1.82-1.953.5640.1112.2121998621561720.9830.1399.3
1.95-2.113.5180.09314.8920054576857000.9860.1198.8
2.11-2.313.480.08116.918209529352330.990.09698.9
2.31-2.583.3450.07218.0315771479347150.9910.08698.4
2.58-2.983.1180.0619.1312860426941240.9930.07396.6
2.98-3.653.4150.04923.1611927354534930.9950.05898.5
3.65-5.163.5680.0425.729679275727130.9970.04798.4
5.16-42.833.4210.03924.945090151614880.9970.04798.2

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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: 1.15→42.83 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.19352 --
Rwork0.1478 --
obs-65513 95.79 %
Displacement parametersBiso mean: 15.099 Å2
Refinement stepCycle: LAST / Resolution: 1.15→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 20 288 1937

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