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- PDB-2agi: The leupeptin-trypsin covalent complex at 1.14 A resolution -

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Basic information

Entry
Database: PDB / ID: 2agi
TitleThe leupeptin-trypsin covalent complex at 1.14 A resolution
Components
  • beta-trypsin
  • leupeptin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Acyl-enzyme / serine protease / proteinase / peptidase / hydrolase / 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
LEUPEPTIN / : / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: 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 / 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_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.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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: beta-trypsin
A: leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9865
Polymers23,7542
Non-polymers2323
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.888, 63.562, 69.102
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 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: Protein/peptide leupeptin


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
References: NOR: NOR00487, LEUPEPTIN
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LEUPEPTIN IS COVALENTLY CONNECTED TO ACTIVE_SITE SER 195 OF THE ENZYME TO FORM A HEMIACETAL.
Has protein modificationY
Sequence detailsTHERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ...THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ONE RESIDUE. SO THE DBREF WILL REPORT 4 PDB RESIDUES MATCHING NORINE 3 RESIDUE

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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 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→46.63 Å / Num. all: 88464 / Num. obs: 88464 / % possible obs: 99.64 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 13.1
Reflection shellResolution: 1.14→1.2 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6920 / Rsym value: 0.284

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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 2AGE

2age


Resolution: 1.14→46.63 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.808 / SU ML: 0.016 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / 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 4449 5 %inherited from PDB entry 2AGE
Rwork0.116 ---
all0.117 88464 --
obs0.117 88464 99.64 %-
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: 12.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.14→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 11 371 2036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211762
X-RAY DIFFRACTIONr_bond_other_d0.0070.021542
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.972381
X-RAY DIFFRACTIONr_angle_other_deg1.90433638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09826.06661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30915294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.996152
X-RAY DIFFRACTIONr_chiral_restr0.1370.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021882
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02310
X-RAY DIFFRACTIONr_nbd_refined0.3770.2346
X-RAY DIFFRACTIONr_nbd_other0.270.21807
X-RAY DIFFRACTIONr_nbtor_other0.1020.2977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2255
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3560.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.230
X-RAY DIFFRACTIONr_mcbond_it3.08321166
X-RAY DIFFRACTIONr_mcbond_other2.1982475
X-RAY DIFFRACTIONr_mcangle_it3.97731829
X-RAY DIFFRACTIONr_scbond_it5.2834.5690
X-RAY DIFFRACTIONr_scangle_it6.736546
X-RAY DIFFRACTIONr_rigid_bond_restr3.47133616
X-RAY DIFFRACTIONr_sphericity_free16.9765372
X-RAY DIFFRACTIONr_sphericity_bonded6.87553265
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.386 152
Rwork0.356 2669
all-2821

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