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- PDB-9p77: Structure of Bovine Trypsin Complexed with Mellitic Acid at Room ... -

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Basic information

Entry
Database: PDB / ID: 9p77
TitleStructure of Bovine Trypsin Complexed with Mellitic Acid at Room Temperature
ComponentsPretrypsinogen I
KeywordsHYDROLASE / protease / trypsin / crystallization / additives / carboxylic acids
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 / MALONATE ION / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 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

Downloads & links

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Assembly

Deposited unit
B: Pretrypsinogen I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8718
Polymers25,8061
Non-polymers1,0657
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.200, 69.200, 75.270
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
11B-303-

ACT

21B-306-

BHC

31B-306-

BHC

41B-306-

BHC

51B-306-

BHC

61B-550-

HOH

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Components

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Protein , 1 types, 1 molecules B

#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 , 6 types, 204 molecules

#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 38.99 % / Description: trigonal prisms
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: vapor diffusion at pH 6.0 with 50% TACSIMATE as reservoir precipitant. 6 ul droplets, 0.50 ml reservoirs. Drops 50% 40 mg/ml protein stock and 50% reservoir. Room temperature
PH range: 6.5

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Data collection

DiffractionMean temperature: 292 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54 Å
DetectorType: RIGAKU AFC9 / Detector: IMAGE PLATE / Date: Apr 16, 2012 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.3→38.8 Å / Num. obs: 43964 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.9
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 430

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.6 Å / SU ML: 0.3582 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 39.5202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 1998 4.54 %
Rwork0.1687 41966 -
obs0.1706 43964 85.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.69 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 73 197 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751756
X-RAY DIFFRACTIONf_angle_d0.7492387
X-RAY DIFFRACTIONf_chiral_restr0.0758262
X-RAY DIFFRACTIONf_plane_restr0.0054312
X-RAY DIFFRACTIONf_dihedral_angle_d12.7272618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.5747280.6073599X-RAY DIFFRACTION17.38
1.34-1.370.5627760.53171704X-RAY DIFFRACTION49.53
1.37-1.410.57521250.51412609X-RAY DIFFRACTION75.57
1.41-1.460.47111370.4642919X-RAY DIFFRACTION84.49
1.46-1.510.45871530.39543138X-RAY DIFFRACTION91.54
1.51-1.570.36481530.36743240X-RAY DIFFRACTION92.68
1.57-1.640.41641620.32193285X-RAY DIFFRACTION95.72
1.64-1.730.29371650.25623391X-RAY DIFFRACTION97.69
1.73-1.840.27461630.21563452X-RAY DIFFRACTION99.31
1.84-1.980.24331660.20483459X-RAY DIFFRACTION99.67
1.98-2.180.21571630.17083486X-RAY DIFFRACTION99.62
2.18-2.50.2321660.15753506X-RAY DIFFRACTION99.76
2.5-3.140.17781690.15443534X-RAY DIFFRACTION99.46
3.14-34.60.14621720.11093644X-RAY DIFFRACTION99.22

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