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- PDB-9bkg: Crystal structure of selenomethionine labeled bovine trypsin muta... -

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Basic information

Entry
Database: PDB / ID: 9bkg
TitleCrystal structure of selenomethionine labeled bovine trypsin mutant - S195A solved by Sulphur-SAD at 1.54A wavelength
ComponentsSerine protease 1
KeywordsHYDROLASE / selenomethionine labeled / S195A
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. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.57 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 selenomethionine labeled bovine trypsin mutant - S195A solved by Sulphur-SAD at 1.54A wavelength
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease 1


Theoretical massNumber of molelcules
Total (without water)23,4021
Polymers23,4021
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8900 Å2
Unit cell
Length a, b, c (Å)54.708, 54.708, 107.174
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-538-

HOH

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Components

#1: Protein Serine protease 1 / Anionic trypsin I / Anionic trypsin-I / Beta-trypsin / Cationic trypsin / Pretrypsinogen I / ...Anionic trypsin I / Anionic trypsin-I / Beta-trypsin / Cationic trypsin / Pretrypsinogen I / Trypsin I / Trypsin-I


Mass: 23402.078 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00760, trypsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Imidazole, pH 7.0 , 0.3M Ammonium Sulfate, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 109778 / % possible obs: 84.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 71.38
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.024 / Num. unique obs: 72

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→50 Å / SU ML: 0.1028 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 3805 3.47 %
Rwork0.1857 105973 -
obs0.1864 109778 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 1.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 0 254 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411472
X-RAY DIFFRACTIONf_angle_d0.82271994
X-RAY DIFFRACTIONf_chiral_restr0.0859229
X-RAY DIFFRACTIONf_plane_restr0.0071252
X-RAY DIFFRACTIONf_dihedral_angle_d11.7271515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.26681190.25273575X-RAY DIFFRACTION86.53
1.6-1.630.24611120.24053535X-RAY DIFFRACTION90.81
1.63-1.660.251310.23293659X-RAY DIFFRACTION90.02
1.66-1.690.25261300.22753754X-RAY DIFFRACTION93.46
1.69-1.730.23491320.2253708X-RAY DIFFRACTION94.35
1.73-1.770.23871400.23663935X-RAY DIFFRACTION95.84
1.77-1.810.22061450.21343842X-RAY DIFFRACTION97.01
1.81-1.860.23411420.21293906X-RAY DIFFRACTION97.92
1.86-1.920.19371490.21173977X-RAY DIFFRACTION98.54
1.92-1.980.21241410.20054001X-RAY DIFFRACTION99
1.98-2.050.19811440.19353991X-RAY DIFFRACTION99.59
2.05-2.130.22651460.18933942X-RAY DIFFRACTION99.51
2.13-2.230.21641450.19094020X-RAY DIFFRACTION99.83
2.23-2.350.21871420.19523991X-RAY DIFFRACTION99.71
2.35-2.490.20741370.18744036X-RAY DIFFRACTION99.9
2.49-2.680.21881420.18973964X-RAY DIFFRACTION99.88
2.68-2.950.23251520.1874041X-RAY DIFFRACTION99.88
2.95-3.380.20271380.18023997X-RAY DIFFRACTION99.98
3.38-4.260.1971460.17774015X-RAY DIFFRACTION99.98
4.26-500.20471440.18514039X-RAY DIFFRACTION99.98
Refinement TLS params.Method: refined / Origin x: -19.6484066441 Å / Origin y: 6.04558137597 Å / Origin z: 11.0982130784 Å
111213212223313233
T0.10285689592 Å2-0.0116483328393 Å20.000693734300876 Å2-0.0989617250466 Å2-0.00548023142319 Å2--0.0598226567 Å2
L0.559994187211 °2-0.131837924901 °20.0788369707315 °2-0.650750813076 °2-0.280070913702 °2--0.404564831217 °2
S-0.0205629949407 Å °0.0280712705774 Å °-0.0101499134604 Å °-0.0337698380175 Å °0.00776597630958 Å °-0.0535438357679 Å °0.00628923834192 Å °-0.00281880048386 Å °0.0044582679236 Å °
Refinement TLS groupSelection details: all

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