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- PDB-1oss: T190P STREPTOMYCES GRISEUS TRYPSIN IN COMPLEX WITH BENZAMIDINE -

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Basic information

Entry
Database: PDB / ID: 1oss
TitleT190P STREPTOMYCES GRISEUS TRYPSIN IN COMPLEX WITH BENZAMIDINE
Componentstrypsin
KeywordsHYDROLASE / TRYPSIN / SERINE PROTEASE / MUTANT
Function / homology
Function and homology information


trypsin / serine-type endopeptidase activity / proteolysis
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 / Trypsin-like serine proteases ...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 / Trypsin
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 1.93 Å
AuthorsPage, M.J. / Wong, S.L. / Hewitt, J. / Strynadka, N.C. / MacGillivray, R.T.
Citation
Journal: Biochemistry / Year: 2003
Title: Engineering the Primary Substrate Specificity of Streptomyces griseus Trypsin.
Authors: Page, M.J. / Wong, S.L. / Hewitt, J. / Strynadka, N.C. / MacGillivray, R.T.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Refined Crystal Structure of Streptomyces Griseus Trypsin at 1.7 Angstroms Resolution
Authors: Read, R.J. / James, M.N.G.
#2: Journal: Biochemistry / Year: 1984
Title: Critical Comparison of Comparative Model Building of Streptomyces Griseus Trypsin
Authors: Read, R.J. / Brayer, G.D. / Jurasek, L. / James, M.N.G.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AMINO ACID NUMBERING IS BASED ON CHYMOTRYPSINOGEN AND IS THE SAME AS THAT USED IN THE ...SEQUENCE AMINO ACID NUMBERING IS BASED ON CHYMOTRYPSINOGEN AND IS THE SAME AS THAT USED IN THE NATIVE STRUCTURE (PDB ID 1SGT).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4715
Polymers23,1191
Non-polymers3524
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.079, 69.601, 119.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein trypsin / SGT


Mass: 23118.799 Da / Num. of mol.: 1 / Mutation: T190P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: SPRT / Plasmid: PWB980 / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB700 / References: UniProt: P00775, trypsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BEN / BENZAMIDINE


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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.55 M AMMONIUM SULPHATE, 10 MM CALCIUM ACETATE , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
21.5 Mammonium sulfate1drop
310 mMcalcium acetate1droppH6.2
41.55 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 2002
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 16130 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.031
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.056 / % possible all: 79.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 14471
Reflection shell
*PLUS
Lowest resolution: 2.05 Å / % possible obs: 79.1 % / Mean I/σ(I) obs: 25.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
XTALVIEWrefinement
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1SGT

1sgt


Resolution: 1.93→19.86 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESIDUES 165 AND 192 HAVE TWO ALTERNATE CONFORMATIONS THAT ARE CLEARLY VISIBLE IN THE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 726 5 %RANDOM
Rwork0.167 ---
obs0.167 16130 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6589 Å2 / ksol: 0.442522 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--2.67 Å20 Å2
3----2.09 Å2
Refine analyzeLuzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.93→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 20 193 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2 95 4.6 %
Rwork0.145 1988 -
obs--79.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4BEN_XPLOR_PAR.TXTBEN_XPLOR_TOP.TXT
Software
*PLUS
Name: XTALVIEW / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg25.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.89
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.2

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