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- PDB-9pct: Structure of Porcine Trypsin Crystals Grown from PEG Complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9pct
TitleStructure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization Additives III
ComponentsTrypsin
KeywordsPEPTIDE BINDING PROTEIN / sucrose / crystallization / additives / Silver Bullets / organic acids / ligands
Function / homology
Function and homology information


trypsin / digestion / 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 / 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
ACETATE ION / BENZAMIDINE / CITRATE ANION / D-MALATE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6 / PHOSPHATE ION / D(-)-TARTARIC ACID / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization Additives III
Authors: McPherson, A.
History
DepositionJun 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,14439
Polymers24,4281
Non-polymers5,71638
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.820, 58.820, 135.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-316-

PO4

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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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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 14 types, 190 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O4
#11: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#12: 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
#13: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#14: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#15: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#16: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 48.66 % / Description: rectangular prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs of 30% PEG 3350 buffered at pH 6.5 with 0.1 M HEPES. Drops 3 ul of reservoir, 2 ul of additive mix ( TACSIMATE, ...Details: Sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs of 30% PEG 3350 buffered at pH 6.5 with 0.1 M HEPES. Drops 3 ul of reservoir, 2 ul of additive mix ( TACSIMATE, glycerol, sucrose, sorbitol), 3 ul of 40 mg/ml stock protein solution buffered at pH 6.5 with 0.1 M HEPES.

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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 12, 2012 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.41→27.1 Å / Num. obs: 36756 / % possible obs: 78.7 % / Redundancy: 3.41 % / Biso Wilson estimate: 18.65 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.5
Reflection shellResolution: 1.41→1.46 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2 / 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: 1.41→26.31 Å / SU ML: 0.1247 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 18.0863
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
Rfree0.1698 2547 7.02 %
Rwork0.1312 33750 -
obs0.134 36297 77.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.32 Å2
Refinement stepCycle: LAST / Resolution: 1.41→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 379 154 2175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782099
X-RAY DIFFRACTIONf_angle_d1.33172777
X-RAY DIFFRACTIONf_chiral_restr0.0962297
X-RAY DIFFRACTIONf_plane_restr0.007334
X-RAY DIFFRACTIONf_dihedral_angle_d19.3632887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.440.4251150.3061191X-RAY DIFFRACTION8.09
1.44-1.470.3338360.2799519X-RAY DIFFRACTION21.99
1.47-1.50.2733450.2444809X-RAY DIFFRACTION33.85
1.5-1.530.28241080.21191100X-RAY DIFFRACTION47.17
1.53-1.570.26981480.18491877X-RAY DIFFRACTION79.69
1.57-1.620.20371450.16331981X-RAY DIFFRACTION83.97
1.62-1.660.19181310.14672020X-RAY DIFFRACTION84.09
1.66-1.720.19841480.13892036X-RAY DIFFRACTION85.58
1.72-1.780.17371770.132060X-RAY DIFFRACTION86.57
1.78-1.850.18121600.13342102X-RAY DIFFRACTION88.05
1.85-1.930.18171540.11922164X-RAY DIFFRACTION90.44
1.93-2.030.15661490.11112254X-RAY DIFFRACTION93.39
2.03-2.160.13261720.10232309X-RAY DIFFRACTION95.98
2.16-2.330.14471940.11142362X-RAY DIFFRACTION98.04
2.33-2.560.15291760.1162426X-RAY DIFFRACTION99.62
2.56-2.930.16961860.13392443X-RAY DIFFRACTION99.85
2.93-3.690.17392080.12642459X-RAY DIFFRACTION99.51
3.69-26.310.16561950.14182638X-RAY DIFFRACTION99.65

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