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- PDB-1j8a: CRYSTAL STRUCTURE OF BENZAMIDINE INHIBITED BOVINE PANCREATIC TRYP... -

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Basic information

Entry
Database: PDB / ID: 1j8a
TitleCRYSTAL STRUCTURE OF BENZAMIDINE INHIBITED BOVINE PANCREATIC TRYPSIN AT 105K TO 1.21A RESOLUTION FROM LABORATORY SOURCE WITH HIGH NUMBER OF WATERS MODELLED
ComponentsTRYPSINOGEN, CATIONIC
KeywordsHYDROLASE / PROTEIN-INHIBITOR COMPLEX / HIGH NUMBER OF WATERS / ATOMIC RESOLUTION
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: 1.21 Å
AuthorsCuesta-Seijo, J.A. / Garcia-Granda, S.
CitationJournal: BOL.R.SOC.HIST.NAT.SEC.GEOL. / Year: 2002
Title: Trypsin as a model for high resolution X-ray diffraction in proteins.
Authors: Cuesta-Seijo, J.A. / Garcia-Granda, S.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSINOGEN, CATIONIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0799
Polymers23,3241
Non-polymers7558
Water6,936385
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.275, 58.568, 66.141
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 TRYPSINOGEN, CATIONIC / / BETA-TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: bovine pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 6 types, 393 molecules

#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.: 3 / 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 6000, ammonium sulfate, tris-HCl, benzamidine, calcium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR590 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: ENRAF-NONIUS / Date: Jun 9, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→19.9 Å / Num. all: 64859 / Num. obs: 64859 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.2
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6239 / % possible all: 77.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5PTP

5ptp


Resolution: 1.21→19.9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used maximum likelihood with structure factors target from CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3273 -RANDOM
Rwork0.16 ---
all0.161 64546 --
obs0.161 64546 99.4 %-
Displacement parametersBiso mean: 9.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.1 Å20 Å20.674 Å2
2--0 Å20.138 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.21→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 45 385 2059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.574
X-RAY DIFFRACTIONc_bond_d0.00839
X-RAY DIFFRACTIONc_dihedral_angle_deg25.877
X-RAY DIFFRACTIONc_improper_angle_deg1.023
X-RAY DIFFRACTIONc_mcangle_it1.077
X-RAY DIFFRACTIONc_mcbond_it0.753
X-RAY DIFFRACTIONc_scangle_it1.908
X-RAY DIFFRACTIONc_scbond_it1.453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.21-1.250.2763430.253X-RAY DIFFRACTION623997.5
1.25-1.30.2543330.235X-RAY DIFFRACTION636499.1
1.3-1.360.2023220.213X-RAY DIFFRACTION639899.6
1.36-1.430.1953390.185X-RAY DIFFRACTION640699.7
1.43-1.520.1712990.161X-RAY DIFFRACTION641399.6
1.52-1.640.1563510.147X-RAY DIFFRACTION644199.5
1.64-1.810.1613050.141X-RAY DIFFRACTION643499.4
1.81-2.070.1723230.144X-RAY DIFFRACTION649799.8
2.07-2.610.1643500.14X-RAY DIFFRACTION656599.8
2.61-19.90.163080.146X-RAY DIFFRACTION678999.7

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