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- PDB-2age: Succinyl-AAPR-trypsin acyl-enzyme at 1.15 A resolution -

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Basic information

Entry
Database: PDB / ID: 2age
TitleSuccinyl-AAPR-trypsin acyl-enzyme at 1.15 A resolution
Components
  • Cationic trypsin
  • succinyl-Ala-Ala-Pro-Arg
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACYL-ENZYME / SERINE PROTEASE / PROTEINASE / PEPTIDASE / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
Biological speciesBos taurus (cattle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Aug 23, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.0Apr 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range
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.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_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_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Cationic trypsin
A: succinyl-Ala-Ala-Pro-Arg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8643
Polymers23,8242
Non-polymers401
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.948, 63.720, 69.008
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 Cationic trypsin / E.C.3.4.21.4 / Beta-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: Protein/peptide succinyl-Ala-Ala-Pro-Arg


Mass: 499.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE P-NITROANALINE GROUP IN THE ORIGINAL PEPTIDE LIGAND WAS LOST AS IT MADE THE ACYL_ENZYME COMPLEX. ...THE P-NITROANALINE GROUP IN THE ORIGINAL PEPTIDE LIGAND WAS LOST AS IT MADE THE ACYL_ENZYME COMPLEX. THE COORDINATES OF THIS GROUP WERE NOT PRESENT IN THE DEPOSITED FILE AND WERE NOT BUILT IN THE INHIBITOR IN CHAIN A

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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: 2.81 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6.0, 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: Oct 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→46.63 Å / Num. all: 86942 / Num. obs: 86942 / % possible obs: 99.27 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 9.3
Reflection shellResolution: 1.15→1.21 Å / % possible obs: 0 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.1 / Num. measured obs: 7544 / Rsym value: 0.658

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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 1TLD with solvent removed

1tld


Resolution: 1.15→46.63 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.844 / SU ML: 0.017 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.138 4351 5 %RANDOM
Rwork0.119 ---
all0.12 86941 --
obs0.12 86941 93.56 %-
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: 13.438 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.15→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 1 390 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211739
X-RAY DIFFRACTIONr_bond_other_d0.0040.021503
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9532357
X-RAY DIFFRACTIONr_angle_other_deg2.68733561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27225.73861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51315288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.124153
X-RAY DIFFRACTIONr_chiral_restr0.1510.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021910
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02309
X-RAY DIFFRACTIONr_nbd_refined0.3730.2349
X-RAY DIFFRACTIONr_nbd_other0.2630.21827
X-RAY DIFFRACTIONr_nbtor_other0.0990.21066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2278
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3770.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.224
X-RAY DIFFRACTIONr_mcbond_it3.21221171
X-RAY DIFFRACTIONr_mcbond_other2.3912472
X-RAY DIFFRACTIONr_mcangle_it4.17331827
X-RAY DIFFRACTIONr_scbond_it5.4514.5669
X-RAY DIFFRACTIONr_scangle_it6.6356524
X-RAY DIFFRACTIONr_rigid_bond_restr6.87433561
X-RAY DIFFRACTIONr_sphericity_free17.2935391
X-RAY DIFFRACTIONr_sphericity_bonded8.46253203
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.353 177
Rwork0.335 3012
all-3189

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