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Basic information

Entry
Database: PDB / ID: 4tpy
TitleHigh throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density
ComponentsCationic trypsin
KeywordsHYDROLASE / Thrombin / Serpins / Fibrin
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
BENZAMIDINE / BROMIDE ION / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsTeplitsky, E. / Joshi, K. / Mullen, J.D. / Soares, A.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)P41RR012408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103473 United States
Department of Energy (DOE, United States)LDRD11-008 United States
Citation
Journal: J.Struct.Biol. / Year: 2015
Title: High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density.
Authors: Teplitsky, E. / Joshi, K. / Ericson, D.L. / Scalia, A. / Mullen, J.D. / Sweet, R.M. / Soares, A.S.
#1: Journal: Acta Crystallographica Section D Biological Crystallography
Year: 2014
Title: Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes
Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Ma, M.Y. / Agarwal, R. / Jackimowicz, R. / Allaire, M. / Orville, A.M. / ...Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Ma, M.Y. / Agarwal, R. / Jackimowicz, R. / Allaire, M. / Orville, A.M. / Sweet, R.M. / Soares, A.S.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Data collection
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 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_struct_conn_angle / refine_hist / struct_conn
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.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.value / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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
Revision 1.5Nov 6, 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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,25743
Polymers23,3241
Non-polymers2,93242
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-48 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.677, 58.443, 66.670
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 Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Bromine derivative identified using acoustic droplet ejection to screen 1728 distinct conditions on each micro plate.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 7 types, 427 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.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 30mg/ml trypsin and 10mg/ml benzamidine in buffer (10mM CaCl2, 20mM HEPES pH 7.0) is combined with 1x precipitant (20% PEG 8000, 20mM ammonium s., 100 mM Bis Tris pH 7.0). Vapour diffusion ...Details: 30mg/ml trypsin and 10mg/ml benzamidine in buffer (10mM CaCl2, 20mM HEPES pH 7.0) is combined with 1x precipitant (20% PEG 8000, 20mM ammonium s., 100 mM Bis Tris pH 7.0). Vapour diffusion against 2x precipitant (40% PEG 8000, 40mM ammonium s., 200mM Bis Tris pH 7.0).
PH range: 7.0-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 44900 / Num. obs: 44900 / % possible obs: 90.39 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.41
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.07 / % possible all: 33.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementResolution: 1.3→43.95 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.837 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17227 2346 5 %RANDOM
Rwork0.14211 ---
obs0.14356 44900 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2---0.6 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.3→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 78 385 2092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191843
X-RAY DIFFRACTIONr_bond_other_d0.0020.021724
X-RAY DIFFRACTIONr_angle_refined_deg2.3611.962507
X-RAY DIFFRACTIONr_angle_other_deg1.0734009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45126.12962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61815306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.648152
X-RAY DIFFRACTIONr_chiral_restr0.160.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022144
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3521.108960
X-RAY DIFFRACTIONr_mcbond_other1.341.106958
X-RAY DIFFRACTIONr_mcangle_it2.0181.6731218
X-RAY DIFFRACTIONr_mcangle_other2.0241.6741219
X-RAY DIFFRACTIONr_scbond_it2.6291.318883
X-RAY DIFFRACTIONr_scbond_other2.6291.319883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7691.8571290
X-RAY DIFFRACTIONr_long_range_B_refined6.98612.0822451
X-RAY DIFFRACTIONr_long_range_B_other6.49610.6352267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 67 -
Rwork0.311 1317 -
obs--36.47 %

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