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- PDB-9p7b: The Structure of Bovine Trypsin Complexed With Mellitic Acid at 1... -

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Basic information

Entry
Database: PDB / ID: 9p7b
TitleThe Structure of Bovine Trypsin Complexed With Mellitic Acid at 173 Degrees
ComponentsPretrypsinogen I
KeywordsHYDROLASE / Mellitic Acid / carboxylic acids / crystallization / protease / additives
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / 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
ACETATE ION / BENZAMIDINE / BENZENE HEXACARBOXYLIC ACID / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 20, 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

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Assembly

Deposited unit
A: Pretrypsinogen I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,66313
Polymers25,8061
Non-polymers1,85712
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.235, 68.235, 73.555
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-302-

BHC

21A-302-

BHC

31A-302-

BHC

41A-302-

BHC

51A-307-

BEN

61A-307-

BEN

71A-307-

BEN

81A-676-

HOH

91A-682-

HOH

101A-703-

HOH

111A-709-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pretrypsinogen I / Anionic trypsin I / Anionic trypsin-I / Beta-trypsin / Cationic trypsin / Trypsin I / Trypsin-I / ...Anionic trypsin I / Anionic trypsin-I / Beta-trypsin / Cationic trypsin / Trypsin I / Trypsin-I / Serine protease 1


Mass: 25806.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 7 types, 331 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-BHC / BENZENE HEXACARBOXYLIC ACID


Mass: 342.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H6O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H8N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.18 Å3/Da / Density % sol: 35.79 % / Description: trigonal prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop vapor diffusion in Cryschem plates. 0.5 Reservoirs of 50% TACSIMATE pH 6. Drops 3.5 ul 40 mg/ml protein stock solution plus 3.5 ul of the reservoir. Room temperature.
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→46.07 Å / Num. obs: 31388 / % possible obs: 97.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 26.71 Å2 / Rmerge(I) obs: 0.065 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 480

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.07 Å / SU ML: 0.221 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 32.174
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 1986 6.33 %
Rwork0.2092 29400 -
obs0.212 31386 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 127 319 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411839
X-RAY DIFFRACTIONf_angle_d0.79082498
X-RAY DIFFRACTIONf_chiral_restr0.0519262
X-RAY DIFFRACTIONf_plane_restr0.005323
X-RAY DIFFRACTIONf_dihedral_angle_d13.9702664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.3951450.34192089X-RAY DIFFRACTION99.51
1.54-1.580.34161460.32322103X-RAY DIFFRACTION99.91
1.58-1.630.32891440.30652147X-RAY DIFFRACTION99.74
1.63-1.680.32341410.30282091X-RAY DIFFRACTION99.33
1.68-1.740.35521460.33172136X-RAY DIFFRACTION99.56
1.74-1.810.33341390.30432107X-RAY DIFFRACTION99.38
1.81-1.890.3271430.27432128X-RAY DIFFRACTION98.78
1.89-1.990.35491400.30492028X-RAY DIFFRACTION95.25
1.99-2.110.34821370.29741979X-RAY DIFFRACTION92.6
2.11-2.280.29551400.25582063X-RAY DIFFRACTION95.29
2.28-2.510.25191340.23272016X-RAY DIFFRACTION93.93
2.51-2.870.24661380.19882112X-RAY DIFFRACTION96.77
2.87-3.610.21420.16152160X-RAY DIFFRACTION98.5
3.61-46.070.20281510.14972241X-RAY DIFFRACTION97.63

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