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- PDB-2ah4: guanidinobenzoyl-trypsin acyl-enzyme at 1.13 A resolution -

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Basic information

Entry
Database: PDB / ID: 2ah4
Titleguanidinobenzoyl-trypsin acyl-enzyme at 1.13 A resolution
Componentsbeta-trypsin
KeywordsHYDROLASE / Acyl-enzyme / serine protease / proteinase / peptidase
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
4-carbamimidamidobenzoic acid / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsRadisky, E.S. / Lee, J.M. / Lu, C.J. / Koshland Jr., D.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates
Authors: Radisky, E.S. / Lee, J.M. / Lu, C.J. / Koshland Jr., D.E.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Aug 23, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.pdbx_leaving_atom_flag / _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 2.1Oct 16, 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
X: beta-trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9287
Polymers23,3241
Non-polymers6046
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.446, 57.908, 66.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein beta-trypsin / E.C.3.4.21.4 / Cationic trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GBS / 4-carbamimidamidobenzoic acid / Nafamostat, bound form


Mass: 179.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N3O2
Comment: anticancer, anticoagulant, antivirus, protease inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.19 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, bis-tris propane, calcium chloride, 4-nitrophenyl 4-guanidinobenzoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→43.85 Å / Num. all: 75171 / Num. obs: 75171 / % possible obs: 99.97 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 11.9
Reflection shellResolution: 1.13→1.19 Å / % possible obs: 71.1 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.5 / Num. measured obs: 8087 / Rsym value: 0.533

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
EPMRphasing
REFMAC5.2refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GBT with ligand and solvent removed

1gbt


Resolution: 1.13→43.85 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.877 / SU ML: 0.018 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.146 3830 5.1 %RANDOM
Rwork0.119 ---
all0.12 75169 --
obs0.12 75169 99.97 %-
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: 8.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.39 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.13→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 33 359 2066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211739
X-RAY DIFFRACTIONr_bond_other_d0.0040.021491
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9712353
X-RAY DIFFRACTIONr_angle_other_deg2.68633527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35525.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90315292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.001152
X-RAY DIFFRACTIONr_chiral_restr0.1480.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021886
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02314
X-RAY DIFFRACTIONr_nbd_refined0.3640.2350
X-RAY DIFFRACTIONr_nbd_other0.260.21843
X-RAY DIFFRACTIONr_nbtor_other0.0930.21036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2215
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.242
X-RAY DIFFRACTIONr_mcbond_it2.71921141
X-RAY DIFFRACTIONr_mcbond_other1.4292466
X-RAY DIFFRACTIONr_mcangle_it3.56331789
X-RAY DIFFRACTIONr_scbond_it4.634.5702
X-RAY DIFFRACTIONr_scangle_it5.9316562
X-RAY DIFFRACTIONr_rigid_bond_restr5.55833566
X-RAY DIFFRACTIONr_sphericity_free13.6275360
X-RAY DIFFRACTIONr_sphericity_bonded5.353197
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.326 186
Rwork0.322 3475
all-3661

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