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- PDB-2ayw: Crystal Structure of the complex formed between trypsin and a des... -

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Basic information

Entry
Database: PDB / ID: 2ayw
TitleCrystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution
ComponentsCationic trypsin
KeywordsHYDROLASE / trypsin / benzamidine / inhibitor
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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
BENZAMIDINE / Chem-ONO / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsSherawat, M. / Kaur, P. / Perbandt, M. / Betzel, C. / Slusarchyk, W.A. / Bisacchi, G.S. / Chang, C. / Jacobson, B.L. / Einspahr, H.M. / Singh, T.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.
Authors: Sherawat, M. / Kaur, P. / Perbandt, M. / Betzel, C. / Slusarchyk, W.A. / Bisacchi, G.S. / Chang, C. / Jacobson, B.L. / Einspahr, H.M. / Singh, T.P.
History
DepositionSep 9, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8397
Polymers23,3241
Non-polymers1,5156
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.550, 68.550, 73.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 455 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ONO / 2-[2-({[4-(DIAMINOMETHYL)PHENYL]AMINO}CARBONYL)-6-METHOXYPYRIDIN-3-YL]-5-{[(1-FORMYL-2,2-DIMETHYLPROPYL)AMINO]CARBONYL}BENZOIC ACID


Mass: 533.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31N5O6
#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5mM MES, 1mM CaCl2, 2.5mM benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 12, 2000 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 0.97→20 Å / Num. all: 225251 / Num. obs: 116664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.66 Å2 / Rsym value: 0.065 / Net I/σ(I): 18.2
Reflection shellResolution: 0.97→1 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.401 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRT

1jrt


Resolution: 0.97→20 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.589 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15683 1167 1 %RANDOM
Rwork0.13355 ---
all0.13773 116664 --
obs0.13773 114997 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 105 449 2183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211787
X-RAY DIFFRACTIONr_bond_other_d0.0020.021518
X-RAY DIFFRACTIONr_angle_refined_deg1.662.012426
X-RAY DIFFRACTIONr_angle_other_deg2.90833569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97325.59359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23615280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.526153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
X-RAY DIFFRACTIONr_nbd_refined0.2060.2367
X-RAY DIFFRACTIONr_nbd_other0.1910.21502
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2913
X-RAY DIFFRACTIONr_nbtor_other0.0940.2951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.2124
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2841.51128
X-RAY DIFFRACTIONr_mcbond_other0.5481.5468
X-RAY DIFFRACTIONr_mcangle_it1.79421772
X-RAY DIFFRACTIONr_scbond_it3.0383841
X-RAY DIFFRACTIONr_scangle_it3.274.5654
X-RAY DIFFRACTIONr_rigid_bond_restr1.94533791
X-RAY DIFFRACTIONr_sphericity_free5.5173450
X-RAY DIFFRACTIONr_sphericity_bonded2.54633265
LS refinement shellResolution: 0.973→0.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 78 -
Rwork0.309 8046 -
obs--95.35 %

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