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- PDB-9pd9: The Structure of Porcine Trypsin in Complex with Crystallization ... -

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Basic information

Entry
Database: PDB / ID: 9pd9
TitleThe Structure of Porcine Trypsin in Complex with Crystallization Additives I
ComponentsTrypsin
KeywordsHYDROLASE / crystallization / additives / Silver Bullets / ligands / PEG / trypsin
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 / OXALATE ION / OXAMIC ACID / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6 / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cryst.Growth Des. / Year: 2026
Title: X-ray Diffraction Analyses of Trypsin Crystals Grown in the Presence of Additives
Authors: McPherson, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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)30,40244
Polymers24,4281
Non-polymers5,97443
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.000, 59.000, 139.660
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-561-

HOH

21A-636-

HOH

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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 , 10 types, 279 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 120.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical
ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#8: Chemical ChemComp-A1CHW / 4-aminobenzene-1-sulfonic acid


Mass: 173.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO3S
#9: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3NO3
#10: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O6
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.56 % / 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. Drops 3.0 ul of reservoir, plus 2 ul additives oxalic acid, sulfanilic acid, 4-amino benzoic acid mix, plus 3.0 ul ...Details: Sitting drop vapor diffusion in Cryschem plates. Reservoirs 30% PEG 3350. Drops 3.0 ul of reservoir, plus 2 ul additives oxalic acid, sulfanilic acid, 4-amino benzoic acid mix, plus 3.0 ul of 40 mg/ml stock protein solution of 0.1 M HEPES at 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 FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 6, 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: 1.28→25.9 Å / Num. obs: 58890 / % possible obs: 91.5 % / Redundancy: 5.78 % / Biso Wilson estimate: 17.39 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.5
Reflection shellResolution: 1.28→1.33 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.8 / 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: 1.28→25.25 Å / SU ML: 0.141 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 14.9008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: This structure is reported from an X ray analysis of crystals grown with 30 percent 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 percent 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 completely omitted and only the protein and ligands are included in the model then the clash score is in the low single digits.
RfactorNum. reflection% reflection
Rfree0.1466 5905 10.14 %
Rwork0.1131 52348 -
obs0.1165 58253 90.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.48 Å2
Refinement stepCycle: LAST / Resolution: 1.28→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 400 236 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972193
X-RAY DIFFRACTIONf_angle_d1.19182840
X-RAY DIFFRACTIONf_chiral_restr0.0989282
X-RAY DIFFRACTIONf_plane_restr0.0092343
X-RAY DIFFRACTIONf_dihedral_angle_d20.5303929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.4337340.3753224X-RAY DIFFRACTION12.5
1.3-1.310.3528640.3807580X-RAY DIFFRACTION30.74
1.31-1.330.3597870.3433873X-RAY DIFFRACTION45.82
1.33-1.340.38181310.31781159X-RAY DIFFRACTION60.42
1.34-1.360.32731740.2981578X-RAY DIFFRACTION84.39
1.36-1.380.3251960.26531785X-RAY DIFFRACTION94.2
1.38-1.40.28262200.23771847X-RAY DIFFRACTION97.5
1.4-1.420.25462000.21831850X-RAY DIFFRACTION97.76
1.42-1.440.24932050.19311896X-RAY DIFFRACTION98.55
1.44-1.470.23591920.17781897X-RAY DIFFRACTION99.15
1.47-1.490.2122190.15881873X-RAY DIFFRACTION99.1
1.49-1.520.20272090.15011902X-RAY DIFFRACTION99.25
1.52-1.550.18762350.13631871X-RAY DIFFRACTION99.11
1.55-1.580.17672190.12791874X-RAY DIFFRACTION99.34
1.58-1.610.17292070.12791890X-RAY DIFFRACTION99.24
1.61-1.650.14652030.12621911X-RAY DIFFRACTION99.44
1.65-1.690.16692220.11941912X-RAY DIFFRACTION99.53
1.69-1.740.1762150.11831913X-RAY DIFFRACTION99.63
1.74-1.790.14772350.1011895X-RAY DIFFRACTION99.86
1.79-1.850.14052070.09171940X-RAY DIFFRACTION99.77
1.85-1.910.12942150.08681899X-RAY DIFFRACTION99.91
1.91-1.990.11722070.08211940X-RAY DIFFRACTION99.95
1.99-2.080.10632120.08481928X-RAY DIFFRACTION99.95
2.08-2.190.10762170.08311952X-RAY DIFFRACTION99.86
2.19-2.330.12392170.08941936X-RAY DIFFRACTION99.86
2.33-2.510.14022330.0911950X-RAY DIFFRACTION99.95
2.51-2.760.13312150.11968X-RAY DIFFRACTION99.91
2.76-3.160.13372430.11211964X-RAY DIFFRACTION99.82
3.16-3.970.12132380.09272003X-RAY DIFFRACTION99.56
3.98-25.250.14532340.12042138X-RAY DIFFRACTION99.54

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