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- PDB-3atl: Crystal structure of trypsin complexed with benzamidine -

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Basic information

Entry
Database: PDB / ID: 3atl
TitleCrystal structure of trypsin complexed with benzamidine
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / PROTEIN / INHIBITOR / BOVINE PANCREAS / HYDROLASE-HYDROLASE INHIBITOR complex
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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsYamane, J. / Yao, M. / Tanaka, I.
CitationJournal: J.Appl.Crystallogr. / Year: 2011
Title: In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities
Authors: Yamane, J. / Yao, M. / Zhou, Y. / Hiramatsu, Y. / Fujiwara, K. / Yamaguchi, T. / Yamaguchi, H. / Togame, H. / Tsujishita, H. / Takemoto, H. / Tanaka, I.
History
DepositionJan 5, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7196
Polymers23,3241
Non-polymers3955
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.624, 58.105, 66.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: pancreas / 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M TRIS-HCL, 30% PEG 3350, 0.2M LITHIUM SULFATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 21074 / Num. obs: 21074 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 15.6
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2000 / Rsym value: 0.21 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7T

3a7t


Resolution: 1.74→19.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.754 / SU ML: 0.058 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18752 1059 5.1 %RANDOM
Rwork0.15935 ---
all0.16079 19887 --
obs0.16079 19887 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.82 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.74→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 22 317 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221684
X-RAY DIFFRACTIONr_bond_other_d0.0020.021103
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9542284
X-RAY DIFFRACTIONr_angle_other_deg0.7913.0092702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75725.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64815269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.505152
X-RAY DIFFRACTIONr_chiral_restr0.0640.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
X-RAY DIFFRACTIONr_nbd_refined0.2340.2323
X-RAY DIFFRACTIONr_nbd_other0.190.21170
X-RAY DIFFRACTIONr_nbtor_refined0.170.2839
X-RAY DIFFRACTIONr_nbtor_other0.0840.2843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.242
X-RAY DIFFRACTIONr_mcbond_it0.5021.51139
X-RAY DIFFRACTIONr_mcbond_other0.091.5464
X-RAY DIFFRACTIONr_mcangle_it0.73721766
X-RAY DIFFRACTIONr_scbond_it1.1963648
X-RAY DIFFRACTIONr_scangle_it1.7424.5518
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 74 -
Rwork0.208 1357 -
obs-1357 98.76 %

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