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- PDB-9aw4: Crystal structure of trypsin at 125 Kelvin with benzamidine (trip... -

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Basic information

Entry
Database: PDB / ID: 9aw4
TitleCrystal structure of trypsin at 125 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: 1.499 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 100 Kelvin with benzamidine
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
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.490, 58.282, 66.660
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.: 309 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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: 125 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 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.499→23.989 Å / Num. obs: 34353 / % possible obs: 98.87 % / Redundancy: 10 % / CC1/2: 0.813 / Net I/σ(I): 19.03
Reflection shellResolution: 1.5→23.97 Å / Num. unique obs: 2331 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SAINTdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→23.989 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.164 / SU B: 1.555 / SU ML: 0.057 / Average fsc free: 0.9626 / Average fsc work: 0.9711 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2197 1708 4.972 %
Rwork0.1902 32645 -
all0.192 --
obs-34353 98.869 %
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: 7.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.073 Å20 Å2-0 Å2
2--0.062 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.499→23.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 10 309 1948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121669
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161540
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.7582263
X-RAY DIFFRACTIONr_angle_other_deg0.6131.7263563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.65553
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.5951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55510269
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.9681058
X-RAY DIFFRACTIONr_chiral_restr0.0890.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2180.2308
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21432
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2837
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.2200
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.27
X-RAY DIFFRACTIONr_nbd_other0.1630.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.230
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0250.21
X-RAY DIFFRACTIONr_mcbond_it0.8120.693891
X-RAY DIFFRACTIONr_mcbond_other0.8080.692891
X-RAY DIFFRACTIONr_mcangle_it1.311.2431112
X-RAY DIFFRACTIONr_mcangle_other1.311.2441113
X-RAY DIFFRACTIONr_scbond_it1.4380.797778
X-RAY DIFFRACTIONr_scbond_other1.4370.797779
X-RAY DIFFRACTIONr_scangle_it2.2481.3861151
X-RAY DIFFRACTIONr_scangle_other2.2481.3861151
X-RAY DIFFRACTIONr_lrange_it4.63211.1111998
X-RAY DIFFRACTIONr_lrange_other4.0128.5491882
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
1.499-1.5380.2751150.25223340.25325300.950.95396.79840.227
1.538-1.580.2581030.26222190.26224420.9290.94295.0860.239
1.58-1.6260.261990.23822240.23924050.9310.9596.59040.208
1.626-1.6750.2581030.2221700.22223160.9470.95998.14330.193
1.675-1.730.2531060.20321470.20522690.9520.96899.29480.175
1.73-1.7910.2481220.18720460.19121690.9630.97599.95390.161
1.791-1.8580.2171150.17120040.17421200.9740.9899.95280.147
1.858-1.9330.1831140.18119210.18120360.9770.97999.95090.155
1.933-2.0180.232990.17818610.18119610.9670.97999.9490.151
2.018-2.1160.1931040.17417680.17518750.9750.98199.840.152
2.116-2.230.22760.17717040.17817860.9720.98199.66410.152
2.23-2.3640.201770.17416150.17516960.9740.98199.76420.149
2.364-2.5250.219960.18715070.18916050.9690.97899.87540.164
2.525-2.7250.222790.17714140.1814940.9690.9899.93310.157
2.725-2.9810.21660.19113280.19213940.9720.9771000.167
2.981-3.3270.196550.18712000.18712560.9720.97899.92040.169
3.327-3.8290.245600.18510690.18811310.9650.98199.82320.169
3.829-4.660.139550.1379140.1379690.9890.991000.133
4.66-6.4690.228440.1737330.1767770.9770.9851000.162
6.469-23.9890.285200.2214680.2234890.9620.9799.79550.209

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