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- PDB-9pdc: Porcine Trypsin grown from PEG and Complexed with Crystallization... -

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Basic information

Entry
Database: PDB / ID: 9pdc
TitlePorcine Trypsin grown from PEG and Complexed with Crystallization Additives II
ComponentsTrypsin
KeywordsHYDROLASE / pig / trypsin / crystallization / additives / Silver Bullets / TACSIMATE / PEG
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase activity / proteolysis / : / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
BENZAMIDINE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6 / L(+)-TARTARIC ACID / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cryst.Growth Des. / Year: 2026
Title: X-ray Diffraction Analyses of Trypsin Crystals Grown in the Presence of Additives
Authors: McPherson, A.
History
DepositionJun 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,51346
Polymers24,4281
Non-polymers6,08545
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.040, 54.010, 77.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Trypsin


Mass: 24428.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: P00761, trypsin

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Non-polymers , 8 types, 233 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 38.9 % / Description: orthorhombic prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop vapor diffusion in Cryschem plates. Reservoirs 30% PEG 3350 buffered with 0.1 M HEPES at pH 6.5. Drops 3 ul of reservoir, 2 ul of additive mix ( TACSIMATE, PEG 3350), 3 ul of 40 ...Details: Sitting drop vapor diffusion in Cryschem plates. Reservoirs 30% PEG 3350 buffered with 0.1 M HEPES at pH 6.5. Drops 3 ul of reservoir, 2 ul of additive mix ( TACSIMATE, PEG 3350), 3 ul of 40 mg/ml stock protein solution buffered with 0.1 M HEPES pH 6.5.
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 9, 2012
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.27→26.1 Å / Num. obs: 44379 / % possible obs: 78.6 % / Redundancy: 3.19 % / Biso Wilson estimate: 14.47 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.9
Reflection shellResolution: 1.27→1.29 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 800

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→23.29 Å / SU ML: 0.1158 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 18.3502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: This structure is reported from an X-ray analysis of crystals grown with 30% PEG as the precipitating agent and was refined using REFINE from the PHENIX system. It was assumed in this ...Details: This structure is reported from an X-ray analysis of crystals grown with 30% PEG as the precipitating agent and was refined using REFINE from the PHENIX system. It was assumed in this refinement and thought appropriate to treat the solvent regions as mixtures or amalgams of disordered water molecules, ordered molecules of water, and PEG molecules of short, different lengths. The inclusion of a large number of PEG molecules is consistent with data indicating that PEG constitutes a large volume of the non protein occupied crystal, with previous reports in the literature of PEG constituents of the solvent regions, and with the strand like appearance of the low level electron density in the solvent regions. Because all of the PEG molecules included here are of low to moderate occupancy, and the clash analysis neglects this property, the clash score reported by REFINE and by the PDB in the validation report is erroneous and should be disregarded. It is not a valid representation of reality. In addition, automated approaches to placing water molecules in crystals grown from PEG, are not to be trusted. If the PEG molecules are omitted from the model and only the protein and ligands are included then the clash score is in the low single digits.
RfactorNum. reflection% reflection
Rfree0.1541 2159 4.98 %
Rwork0.1206 41204 -
obs0.1223 43363 82.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.18 Å2
Refinement stepCycle: LAST / Resolution: 1.27→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 404 188 2234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752147
X-RAY DIFFRACTIONf_angle_d1.09232738
X-RAY DIFFRACTIONf_chiral_restr0.0861275
X-RAY DIFFRACTIONf_plane_restr0.007311
X-RAY DIFFRACTIONf_dihedral_angle_d21.6134924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.30.3334640.29381175X-RAY DIFFRACTION35.92
1.3-1.330.28891190.22812053X-RAY DIFFRACTION62.31
1.33-1.370.20751030.19122258X-RAY DIFFRACTION68.51
1.37-1.410.23091450.18582436X-RAY DIFFRACTION74
1.41-1.450.25721380.17632594X-RAY DIFFRACTION78.66
1.45-1.510.20831750.15812692X-RAY DIFFRACTION82.41
1.51-1.570.21031260.15932935X-RAY DIFFRACTION87.66
1.57-1.640.19081370.14582955X-RAY DIFFRACTION88.9
1.64-1.720.17251650.1343014X-RAY DIFFRACTION90.83
1.72-1.830.1591470.12123075X-RAY DIFFRACTION91.93
1.83-1.970.14111830.09683101X-RAY DIFFRACTION93.3
1.97-2.170.13211690.09153156X-RAY DIFFRACTION94.14
2.17-2.490.11911790.09343222X-RAY DIFFRACTION95.64
2.49-3.130.15131570.11323288X-RAY DIFFRACTION95.83
3.13-23.290.13661520.123250X-RAY DIFFRACTION90.91

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