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- PDB-9bom: Crystal structure of reduced bovine trypsin, 25mM DTT-treated -

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Basic information

Entry
Database: PDB / ID: 9bom
TitleCrystal structure of reduced bovine trypsin, 25mM 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 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 / 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, 25mM 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
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)23,4442
Polymers23,3241
Non-polymers1201
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.424, 54.424, 106.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-637-

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.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Imidazole pH 7.0, 0.3M ammonium sulfate, 30% PEG-8000

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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: 40795 / % possible obs: 98.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 40.07
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 0.826 / Num. unique obs: 1954

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→28.44 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.39 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 1915 4.9 %
Rwork0.176 --
obs0.1767 39087 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 9 249 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051669
X-RAY DIFFRACTIONf_angle_d0.7732263
X-RAY DIFFRACTIONf_dihedral_angle_d12.101587
X-RAY DIFFRACTIONf_chiral_restr0.081254
X-RAY DIFFRACTIONf_plane_restr0.007291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.28081140.24112241X-RAY DIFFRACTION82
1.38-1.420.22921250.2162410X-RAY DIFFRACTION88
1.42-1.460.21951270.21052481X-RAY DIFFRACTION90
1.46-1.510.22751320.19572552X-RAY DIFFRACTION92
1.51-1.560.22451290.19752564X-RAY DIFFRACTION93
1.56-1.630.23821350.18562612X-RAY DIFFRACTION94
1.63-1.70.20381390.18212703X-RAY DIFFRACTION97
1.7-1.790.17221430.16352668X-RAY DIFFRACTION97
1.79-1.90.2251460.18012750X-RAY DIFFRACTION98
1.9-2.050.19131390.17022764X-RAY DIFFRACTION99
2.05-2.250.18651400.17152782X-RAY DIFFRACTION99
2.25-2.580.18331500.17232818X-RAY DIFFRACTION100
2.58-3.250.17521450.18292850X-RAY DIFFRACTION99
3.25-28.440.16331510.16032977X-RAY DIFFRACTION100

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