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- PDB-1s85: PORCINE TRYPSIN COMPLEXED WITH P-HYDROXYMETHYL BENZAMIDINE AND BORATE -

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Basic information

Entry
Database: PDB / ID: 1s85
TitlePORCINE TRYPSIN COMPLEXED WITH P-HYDROXYMETHYL BENZAMIDINE AND BORATE
ComponentsTRYPSIN
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


trypsin / digestion / 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
[4-(1,3,2-DIOXABOROLAN-2-YLOXY)METHYL]BENZAMIDINE / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTransue, T.R. / Krahn, J.M. / Gabel, S.A. / Derose, E.F. / London, R.E.
CitationJournal: Biochemistry / Year: 2004
Title: X-ray and NMR characterization of covalent complexes of trypsin, borate, and alcohols.
Authors: Transue, T.R. / Krahn, J.M. / Gabel, S.A. / DeRose, E.F. / London, R.E.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8514
Polymers23,4931
Non-polymers3573
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.844, 55.410, 46.930
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 TRYPSIN


Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761, 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SBZ / [4-(1,3,2-DIOXABOROLAN-2-YLOXY)METHYL]BENZAMIDINE


Mass: 221.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14BN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.8M MgCl2, 50mM HEPES, 5mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
2100 mMG3P1drop
41.6-1.8 M1reservoirMgSO4
550 mMHEPES1reservoiror Tris
65 mM1reservoirCaCl2
31dropNaOHpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 2002 / Details: MSC/YALE DOUBLE FOCUSING MIRRORS
RadiationMonochromator: MSC/YALE DOUBLE FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 10156 / Num. obs: 10156 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.325 % / Rsym value: 0.111 / Net I/σ(I): 20.4867
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.72 % / Mean I/σ(I) obs: 6.391 / Num. unique all: 1038 / Rsym value: 0.377 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 99.8 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKS

1aks


Resolution: 2.2→100 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: AMBER98
RfactorNum. reflection% reflectionSelection details
Rfree0.254 540 -RANDOM
Rwork0.212 ---
obs-10156 96.5 %-
Displacement parametersBiso mean: 25.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.383 Å20 Å20 Å2
2---5.713 Å20 Å2
3---4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 36 780 4233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.83
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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