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- PDB-2oxs: Crystal Structure of the trypsin complex with benzamidine at high... -

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Basic information

Entry
Database: PDB / ID: 2oxs
TitleCrystal Structure of the trypsin complex with benzamidine at high temperature (35 C)
ComponentsCationic trypsin
KeywordsHYDROLASE / trypsin / benzamidine / high temperature / crystsl structure
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
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsAlok, A. / Sinha, M. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the trypsin complex with benzamidine at high temperature (35 C)
Authors: Alok, A. / Sinha, M. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2016Group: Structure summary
Revision 1.4Dec 28, 2016Group: Database references
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Oct 25, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5814
Polymers23,3241
Non-polymers2563
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.756, 58.484, 67.406
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 Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 308 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 9000, 2,5mM benzamidine, ammonium sulphate. CaCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 308K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2006 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 51449 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.26 / Net I/σ(I): 42.2
Reflection shellResolution: 1.32→1.34 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AYW

2ayw


Resolution: 1.32→44.19 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.633 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15814 1059 2.1 %RANDOM
Rwork0.15533 ---
all0.156 51449 --
obs0.15539 50390 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.288 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.32→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 15 235 1878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221681
X-RAY DIFFRACTIONr_bond_other_d0.0130.021103
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9552264
X-RAY DIFFRACTIONr_angle_other_deg2.793.0092717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26625.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.238152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_nbd_refined0.3980.2339
X-RAY DIFFRACTIONr_nbd_other0.2120.21141
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2829
X-RAY DIFFRACTIONr_nbtor_other0.0950.2910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0421.51118
X-RAY DIFFRACTIONr_mcbond_other0.211.5466
X-RAY DIFFRACTIONr_mcangle_it1.56321741
X-RAY DIFFRACTIONr_scbond_it2.3713655
X-RAY DIFFRACTIONr_scangle_it3.3344.5523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 85 -
Rwork0.21 3649 -
obs--99.63 %

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