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- PDB-9bok: Crystal structure of reduced bovine trypsin, 50mM DTT-treated -

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Basic information

Entry
Database: PDB / ID: 9bok
TitleCrystal structure of reduced bovine trypsin, 50mM DTT-treated
ComponentsCationic trypsin
KeywordsHYDROLASE / reduced trypsin / DTT
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 domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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 domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of reduced bovine trypsin, 50mM DTT-treated
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionMay 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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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)23,4442
Polymers23,3241
Non-polymers1201
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.428, 54.428, 107.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

21A-642-

HOH

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Imidazole pH 7.0, 30% PEG-8000, 0.3M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 40294 / % possible obs: 97.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 13.23 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.94
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 0.786 / Num. unique obs: 1866

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→26.38 Å / SU ML: 0.1212 / Cross valid method: FREE R-VALUE / σ(F): 0.27 / Phase error: 19.5407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1923 1945 5.12 %
Rwork0.1704 36061 -
obs0.1715 38006 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.45 Å2
Refinement stepCycle: LAST / Resolution: 1.35→26.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 9 250 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531669
X-RAY DIFFRACTIONf_angle_d0.80722263
X-RAY DIFFRACTIONf_chiral_restr0.0834254
X-RAY DIFFRACTIONf_plane_restr0.0069291
X-RAY DIFFRACTIONf_dihedral_angle_d11.7716587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.2282990.24991714X-RAY DIFFRACTION62.45
1.38-1.420.23841120.21322041X-RAY DIFFRACTION74.47
1.42-1.460.21120.20712227X-RAY DIFFRACTION80.13
1.46-1.510.25031280.18932436X-RAY DIFFRACTION87
1.51-1.560.23421410.18892586X-RAY DIFFRACTION92.79
1.56-1.620.20331440.17742601X-RAY DIFFRACTION94.46
1.62-1.70.20761470.17952717X-RAY DIFFRACTION96.76
1.7-1.790.18081450.17212709X-RAY DIFFRACTION97.71
1.79-1.90.19811540.16992724X-RAY DIFFRACTION98.29
1.9-2.040.18131490.16012795X-RAY DIFFRACTION98.96
2.04-2.250.1721500.16352813X-RAY DIFFRACTION99.23
2.25-2.570.17721470.16672822X-RAY DIFFRACTION99.63
2.58-3.240.19181550.17492879X-RAY DIFFRACTION99.84
3.24-26.380.19071620.15852997X-RAY DIFFRACTION99.72

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