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- PDB-9pda: Structure of Porcine Trypsin Crystals Grown From PEG and Complexe... -

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Basic information

Entry
Database: PDB / ID: 9pda
TitleStructure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization Additives IV
ComponentsTrypsin
KeywordsPEPTIDE BINDING PROTEIN / Crystallization / additives / PEG / Silver Bullets / ligands / solvent regions / refinement
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
BENZAMIDINE / MALONATE ION / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6 / PYROMELLITIC ACID / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization Additives IV
Authors: McPherson, A.
History
DepositionJun 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: 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
B: Trypsin
C: Trypsin
D: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,919120
Polymers97,7144
Non-polymers15,205116
Water22,6451257
1
A: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,11820
Polymers24,4281
Non-polymers2,68919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,39132
Polymers24,4281
Non-polymers3,96231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08929
Polymers24,4281
Non-polymers3,66028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,32139
Polymers24,4281
Non-polymers4,89338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.660, 50.720, 125.690
Angle α, β, γ (deg.)90.000, 99.520, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Trypsin


Mass: 24428.424 Da / Num. of mol.: 4
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 , 11 types, 1373 molecules

#2: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical
ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18O4
#4: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#5: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H2O4
#8: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PMA / PYROMELLITIC ACID


Mass: 254.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6O8 / Feature type: SUBJECT OF INVESTIGATION
#10: 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 / Comment: pH buffer*YM
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1257 / 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: 2.35 Å3/Da / Density % sol: 45.89 % / Description: monoclinic prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Sitting drop vapor diffusion in Cryschem plates with reservoirs of 30% PEG 3350 buffered at pH 6.5 with 0.1 M HEPES. Drops composed of 3 ul reservoir, 2 ul of additive mix (oxalic acid, ...Details: Sitting drop vapor diffusion in Cryschem plates with reservoirs of 30% PEG 3350 buffered at pH 6.5 with 0.1 M HEPES. Drops composed of 3 ul reservoir, 2 ul of additive mix (oxalic acid, malic acid, oxaloacetic acid, pyromellitic acid), and 3 ul of a 40 mg/ml protein stock

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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: Jul 4, 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: 1.18→48.17 Å / Num. obs: 288012 / % possible obs: 91.06 % / Redundancy: 4.81 % / Biso Wilson estimate: 15.47 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.3
Reflection shellResolution: 1.18→1.22 Å / Rmerge(I) obs: 0.346 / 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: 1.18→39.25 Å / SU ML: 0.1897 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 28.2162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 13008 4.96 %
Rwork0.1948 249236 -
obs0.1965 262244 91.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.49 Å2
Refinement stepCycle: LAST / Resolution: 1.18→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 1012 1257 8837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01177679
X-RAY DIFFRACTIONf_angle_d1.279710068
X-RAY DIFFRACTIONf_chiral_restr0.09951032
X-RAY DIFFRACTIONf_plane_restr0.01011241
X-RAY DIFFRACTIONf_dihedral_angle_d19.0153005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.42584330.42387648X-RAY DIFFRACTION85.1
1.19-1.210.39334200.40147705X-RAY DIFFRACTION84.86
1.21-1.220.41463900.39037717X-RAY DIFFRACTION85.35
1.22-1.240.3943990.38977946X-RAY DIFFRACTION86.96
1.24-1.250.38953700.35747820X-RAY DIFFRACTION86.58
1.25-1.270.3674130.35187944X-RAY DIFFRACTION87
1.27-1.290.37354740.33967925X-RAY DIFFRACTION88.01
1.29-1.310.36074010.32858074X-RAY DIFFRACTION88.52
1.31-1.330.34424160.29878194X-RAY DIFFRACTION89.91
1.33-1.350.31424550.27998109X-RAY DIFFRACTION90.02
1.35-1.370.31744450.26628263X-RAY DIFFRACTION90.57
1.37-1.40.28133680.23998297X-RAY DIFFRACTION90.62
1.4-1.430.2684590.21768291X-RAY DIFFRACTION91.49
1.43-1.460.27354450.2098323X-RAY DIFFRACTION91.62
1.46-1.490.24434560.19758398X-RAY DIFFRACTION92.57
1.49-1.520.24194470.18688334X-RAY DIFFRACTION91.92
1.52-1.560.22664260.17248466X-RAY DIFFRACTION92.9
1.56-1.60.21934690.1628519X-RAY DIFFRACTION93.52
1.6-1.650.22584460.15898543X-RAY DIFFRACTION93.61
1.65-1.70.21924710.15458471X-RAY DIFFRACTION93.21
1.7-1.760.19964540.14798548X-RAY DIFFRACTION93.81
1.76-1.830.20444230.14978534X-RAY DIFFRACTION93.54
1.83-1.920.1974520.15088556X-RAY DIFFRACTION93.65
1.92-2.020.20444170.15248571X-RAY DIFFRACTION92.87
2.02-2.140.21354460.17638208X-RAY DIFFRACTION90.22
2.14-2.310.22064150.18868040X-RAY DIFFRACTION87.5
2.31-2.540.22494510.19078366X-RAY DIFFRACTION91.18
2.54-2.910.21614670.18339058X-RAY DIFFRACTION98.67
2.91-3.670.20064340.17169205X-RAY DIFFRACTION98.75
3.67-39.250.21594460.19739163X-RAY DIFFRACTION96.67

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