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- PDB-1os8: RECOMBINANT STREPTOMYCES GRISEUS TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1os8
TitleRECOMBINANT STREPTOMYCES GRISEUS TRYPSIN
Componentstrypsin
KeywordsHYDROLASE / TRYPSIN / SERINE PROTEASE
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
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 1.55 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 18, 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 1.3Aug 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
Revision 1.4Nov 13, 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)23,2593
Polymers23,1231
Non-polymers1362
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.041, 69.824, 119.654
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: 23122.787 Da / Num. of mol.: 1
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.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 38.73 %
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
Method: microdialysis / Details: Read, R.J., (1988) J.Mol.Biol., 200, 523.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 mM1reservoirCa(CH3CO2)2
30.1 mM1reservoirNaN3
40.5 M1drop(NH4)2SO4

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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 20, 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: 1.55→25 Å / Num. all: 73616 / Num. obs: 26599 / % possible obs: 86.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 20.4
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 5.1 / % possible all: 74.1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 25923 / % possible obs: 84.1 % / Redundancy: 2.8 %
Reflection shell
*PLUS
Lowest resolution: 1.65 Å / % possible obs: 74.1 %

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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: 1.55→13.92 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1252 4.8 %RANDOM
Rwork0.196 ---
obs0.196 25923 84.1 %-
all-73616 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8134 Å2 / ksol: 0.415275 e/Å3
Displacement parametersBiso mean: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--1.82 Å20 Å2
3----2.58 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.55→13.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 6 211 1845
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_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.462
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 169 4.5 %
Rwork0.217 3587 -
obs--74.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: XTALVIEW / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 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_deg25.9
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.91
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scangle_it

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