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- PDB-2a32: Trypsin in complex with benzene boronic acid -

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Basic information

Entry
Database: PDB / ID: 2a32
TitleTrypsin in complex with benzene boronic acid
ComponentsTrypsin
KeywordsHYDROLASE
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 / 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
BORATE ION / PHENYL BORONIC ACID / GUANIDINE-3-PROPANOL / Trypsin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTransue, T.R. / Gabel, S.A. / London, R.E.
Citation
Journal: Bioconjug.Chem. / Year: 2006
Title: NMR and crystallographic characterization of adventitious borate binding by trypsin.
Authors: Transue, T.R. / Gabel, S.A. / London, R.E.
#1: Journal: 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
DepositionJun 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: 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_conn_type / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)24,4409
Polymers23,4931
Non-polymers9478
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.849, 53.704, 46.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 7 types, 294 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG3 / GUANIDINE-3-PROPANOL


Mass: 118.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N3O
#5: Chemical ChemComp-PBC / PHENYL BORONIC ACID


Mass: 121.930 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7BO2 / Details: CAPS buffer
#6: Chemical ChemComp-BO4 / BORATE ION


Mass: 78.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH4O4
#7: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MgSO4, HEPES, CaCl2, the crystal while grown at pH 8.0 was soaked in a solution at pH 10.5 before freezing and data collection. pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Degrees Kelvin
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 19, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→35.2 Å / Num. all: 31465 / Num. obs: 31465 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.087
Reflection shellResolution: 1.5→1.55 Å / % possible obs: 96 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.1 / Num. measured all: 2981 / Num. measured obs: 2981 / Rsym value: 0.446

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Processing

Software
NameVersionClassificationNB
DENZOHKL2000data reduction
SCALEPACKHKL2000data scaling
CNS1.1refinement
MolProbitymodel building
Omodel building
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S5S

1s5s


Resolution: 1.5→35.2 Å / σ(F): 0 / Stereochemistry target values: AMBER
Details: Author states that the close contacts in remark 500 are covalently bonded to a common atom. Therefore, they are said to be 1-3 neighbors. A 1-2 pair of atoms are covalently bonded to each ...Details: Author states that the close contacts in remark 500 are covalently bonded to a common atom. Therefore, they are said to be 1-3 neighbors. A 1-2 pair of atoms are covalently bonded to each other, and each step along covalent bonds adds to the second number. Since 1-3 atoms are indirectly involved in covalent bonds they can get closer than van der Waals distance (less than 2.2 Angstroms for example) from each other.
RfactorNum. reflectionSelection details
Rfree0.188 1569 RANDOM 5%
Rwork0.158 --
all-29998 -
obs-29998 -
Solvent computationBsol: 56.7 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.674 Å20 Å20 Å2
2---1.259 Å20 Å2
3---1.933 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.5→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 150 975 4554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.02

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