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- PDB-9awa: Crystal structure of trypsin at 150 Kelvin with benzamidine (trip... -

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Basic information

Entry
Database: PDB / ID: 9awa
TitleCrystal structure of trypsin at 150 Kelvin with benzamidine (triplicate)
ComponentsCationic trypsin
KeywordsHYDROLASE / Inhibitor / Benzamidine / Complex / x-ray.
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / 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 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsLima, L.M.T.R. / de Sa Ribeiro, F.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: To Be Published
Title: Crystal structure of trypsin at 150 Kelvin with benzamidine (triplicate)
Authors: Lima, L.M.T.R. / de Sa Ribeiro, F.
History
DepositionMar 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4853
Polymers23,3241
Non-polymers1602
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.651, 57.142, 64.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#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.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54184 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Nov 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.497→24.961 Å / Num. obs: 32520 / % possible obs: 99.3 % / Redundancy: 10 % / CC1/2: 0.718 / Net I/σ(I): 17.53
Reflection shellResolution: 1.5→24.95 Å / Num. unique obs: 1664 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SAINTdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.497→24.961 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.18 / SU B: 1.659 / SU ML: 0.062 / Average fsc free: 0.9598 / Average fsc work: 0.9682 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2377 1664 5.117 %
Rwork0.2018 30856 -
all0.204 --
obs-32520 99.292 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.243 Å2-0 Å20 Å2
2---0.718 Å2-0 Å2
3---0.475 Å2
Refinement stepCycle: LAST / Resolution: 1.497→24.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 10 272 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121669
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161540
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.7582263
X-RAY DIFFRACTIONr_angle_other_deg0.6451.7263563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.76753
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.11451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0110269
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.2251058
X-RAY DIFFRACTIONr_chiral_restr0.0920.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2160.2312
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.21397
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2836
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2950.2169
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.212
X-RAY DIFFRACTIONr_nbd_other0.1780.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_mcbond_it1.361.254891
X-RAY DIFFRACTIONr_mcbond_other1.3581.254891
X-RAY DIFFRACTIONr_mcangle_it1.9542.2591112
X-RAY DIFFRACTIONr_mcangle_other1.9542.261113
X-RAY DIFFRACTIONr_scbond_it2.111.4778
X-RAY DIFFRACTIONr_scbond_other2.1081.399779
X-RAY DIFFRACTIONr_scangle_it3.1372.4761151
X-RAY DIFFRACTIONr_scangle_other3.1372.4761151
X-RAY DIFFRACTIONr_lrange_it4.48217.2521971
X-RAY DIFFRACTIONr_lrange_other4.04914.1981876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.497-1.5360.291060.28321760.28323600.9320.93996.69490.255
1.536-1.5780.2511170.25722020.25623350.9530.94999.31480.229
1.578-1.6240.2661100.23721180.23922420.9540.96199.37560.205
1.624-1.6730.291020.23220800.23521890.9470.96399.68020.2
1.673-1.7280.2371090.21520310.21621450.9680.96999.76690.18
1.728-1.7880.2661010.2119520.21320600.960.97299.66020.176
1.788-1.8550.235950.20718710.20919730.9640.97299.64520.172
1.855-1.9310.263910.20518300.20819310.950.97299.48210.173
1.931-2.0160.293890.22417520.22718450.950.96999.78320.19
2.016-2.1140.201820.21316780.21317730.9730.97399.26680.182
2.114-2.2270.251860.21815950.21916940.9580.97199.23260.188
2.227-2.3610.253860.19714930.215890.9620.97599.37070.168
2.361-2.5220.241870.19314120.19515060.9630.97799.53520.171
2.522-2.7220.195710.19913480.19914230.9740.97699.71890.18
2.722-2.9790.243690.20312360.20513090.9640.97399.69440.184
2.979-3.3240.228750.18211040.18511810.9690.97999.83070.172
3.324-3.8270.213660.17510110.17710790.9720.98399.81460.169
3.827-4.660.223500.1528540.1559070.9720.98699.66920.156
4.66-6.4780.213450.1826860.1847320.9870.98599.86340.189
6.478-24.9610.23270.1984270.24600.9670.97598.69570.219

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