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- PDB-2j9n: Robotically harvested Trypsin complexed with Benzamidine containi... -

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Basic information

Entry
Database: PDB / ID: 2j9n
TitleRobotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts
Components
  • (UNKNOWN PEPTIDE) x 2
  • CATIONIC TRYPSIN
KeywordsHYDROLASE / ROBOTIC HARVEST / INTERMOLECULAR CONTACTS / TRYPSIN / CALCIUM / ZYMOGEN / PROTEASE / DIGESTION / SALMON PROTAMINE PEPTIDES / BENZAMIDINE / METAL-BINDING / SERINE PROTEASE
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 / PHENOL / Serine protease 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsViola, R. / Carman, P. / Walsh, J. / Miller, E. / Benning, M. / Frankel, D. / McPherson, A. / Cudney, R. / Rupp, B.
CitationJournal: J.Appl.Crystallogr. / Year: 2007
Title: Operator Assisted Harvesting of Protein Crystals Using a Universal Micromanipulation Robot.
Authors: Viola, R. / Carman, P. / Walsh, J. / Miller, E. / Benning, M. / Frankel, D. / McPherson, A. / Cudney, R. / Rupp, B.
History
DepositionNov 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 28, 2016Group: Source and taxonomy
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATIONIC TRYPSIN
B: UNKNOWN PEPTIDE
C: UNKNOWN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2137
Polymers24,9353
Non-polymers2774
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.924, 56.695, 66.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ENTRY ALSO CONTAINS TWO SHORT PEPTIDE CHAINS OF UNKNOWN SEQUENCE. THE TRYPSIN MOLECULE IS MONOMERICIN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CATIONIC TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-243 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / Tissue: SMOOTH / References: UniProt: P00760, trypsin

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Protein/peptide , 2 types, 2 molecules BC

#2: Protein/peptide UNKNOWN PEPTIDE


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Protein/peptide UNKNOWN PEPTIDE


Mass: 316.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 212 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#7: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.03 Å3/Da / Density % sol: 39.1 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML ...Details: STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML SALMON SPERM PROTAMINE (SIGMA) DROP: 2 UL STOCK PLUS 2 UL COCKTAIL IN CRYSCHEM PLATES AT 22 DEG C.

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 3, 2006 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→25.09 Å / Num. obs: 31641 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.46 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.37
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.84 / % possible all: 95.9

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Processing

Software
NameVersionClassification
BRUKERdata reduction
SCALEPACKdata scaling
EPMRphasing
SHAKEANDWARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y5B

1y5b


Resolution: 1.5→25.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.134 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WARNING: THE PEPTIDES B AND C MEDIATING INTERMOLECULAR CONTACTS BETWEEN 3 TRYPSIN MONOMERS HAVE BEEN ASSIGNED RESIDUE TYPE UNK. THEY HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WARNING: THE PEPTIDES B AND C MEDIATING INTERMOLECULAR CONTACTS BETWEEN 3 TRYPSIN MONOMERS HAVE BEEN ASSIGNED RESIDUE TYPE UNK. THEY HAVE HIGH B-FACTORS AND ARE INTENDED AS PLACE HOLDERS FOR WHAT WE BELIEVE IS A MIXTURE OF BASIC PROTAMINE PEPTIDES, POLYAMINES, AND OTHER COMPOUNDS FROM THE SALMON PROTAMINE EXTRACT, PROBABLY IN MULTIPLE CONFORMATIONS. SIMILAR CAVEATS APPLY TO THE PHENOL ENTITIES WE BELIEVE ORIGINATE FROM IMPURITIES IN THE PROTAMINE EXTRACT USED AS A CRYSTALLIZATION ADDITIVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1664 5 %RANDOM
Rwork0.154 ---
obs0.155 31363 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 18 208 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221809
X-RAY DIFFRACTIONr_bond_other_d0.0010.021205
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9642451
X-RAY DIFFRACTIONr_angle_other_deg0.8923.0082963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00225.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83315292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.038152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_nbd_refined0.1910.2308
X-RAY DIFFRACTIONr_nbd_other0.1930.21207
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2866
X-RAY DIFFRACTIONr_nbtor_other0.0860.2941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.73951192
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.69171903
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4519646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.88611545
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 130
Rwork0.199 2245

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