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- PDB-1sgt: REFINED CRYSTAL STRUCTURE OF STREPTOMYCES GRISEUS TRYPSIN AT 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 1sgt
TitleREFINED CRYSTAL STRUCTURE OF STREPTOMYCES GRISEUS TRYPSIN AT 1.7 ANGSTROMS RESOLUTION
ComponentsTRYPSIN
KeywordsHYDROLASE (SERINE PROTEINASE)
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 / Resolution: 1.7 Å
AuthorsRead, R.J. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Refined crystal structure of Streptomyces griseus trypsin at 1.7 A resolution.
Authors: Read, R.J. / James, M.N.
#1: 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
DepositionApr 13, 1988Processing site: BNL
Revision 1.0Jul 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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
Remark 700SHEET SHEETS S1 AND S2 ARE BOTH SIX-STRANDED SHEETS FORMING A BETA-BARREL. THIS IS REPRESENTED ON ...SHEET SHEETS S1 AND S2 ARE BOTH SIX-STRANDED SHEETS FORMING A BETA-BARREL. THIS IS REPRESENTED ON THE SHEET RECORDS BELOW BY A SEVEN-STRANDED SHEET WITH THE FIRST AND LAST STRANDS IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1172
Polymers23,0771
Non-polymers401
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.290, 50.980, 120.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: THR 20 - POSSIBLE STATIC DISORDER WITH CHI 1 ROTATED BY -120 DEGREES.
2: ARG 21 - POOR DENSITY FOR GUANIDINIUM GROUP.
3: THR 65 - POSSIBLE STATIC DISORDER WITH CHI 1 ROTATED BY +120 DEGREES.
4: LYS 82 - GOOD DENSITY UP TO NZ WHICH IS NOT VISIBLE. / 5: ARG 84 - NOISY DENSITY BEYOND CD. / 6: LYS 87 - VERY WEAK DENSITY BEYOND CD.
7: THR 98 - POSSIBLE STATIC DISORDER WITH CHI 1 ROTATED BY +120 DEGREES.
8: GLN 110 - NOISY SIDE CHAIN DENSITY. / 9: LYS 122 - WEAK DENSITY BEYOND CG.
10: GLN 133 - CHI 3 ANGLE DIFFICULT TO ESTABLISH FROM DENSITY.
11: ARG 145 - NOISY AND AMBIGUOUS SIDE CHAIN DENSITY, PROJECTING INTO SOLVENT.
12: ASN 174 - LITTLE DENSITY FOR OD1 AND ND2. / 13: GLN 192 - DENSITY NOISY AND WEAK BEYOND CB.
14: ASN 204 - NOISY DENSITY, POSSIBLY DUE TO STATIC DISORDER AROUND CHI 1.
15: ASP 205 - VERY WEAK DENSITY FOR CB, NOISY DENSITY FOR CARBOXYL GROUP.
16: SER 236 - POSSIBLE STATIC DISORDER ABOUT CHI 1.
17: ARG 243 - VERY NOISY DENSITY, SIDE CHAIN PAST CG IS ESSENTIALLY ARBITRARY.
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

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Components

#1: Protein TRYPSIN


Mass: 23076.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / References: UniProt: P00775, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Source detailsSGT IS PURIFIED FROM PRONASE, A COMMERCIAL PRODUCT OBTAINED FROM THE EXTRACELLULAR CULTURE FILTRATE ...SGT IS PURIFIED FROM PRONASE, A COMMERCIAL PRODUCT OBTAINED FROM THE EXTRACELLULAR CULTURE FILTRATE OF THE SOIL BACTERIUM STREPTOMYCES GRISEUS, STRAIN K1.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal grow
*PLUS
pH: 6.2 / Method: microdialysis
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

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 24878 / Num. measured all: 25580
Reflection shell
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→8 Å / σ(I): 0
RfactorNum. reflection% reflection
all0.23 --
obs0.161 20046 80.6 %
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 1 192 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.014
X-RAY DIFFRACTIONp_angle_d0.0380.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.027
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8161.5
X-RAY DIFFRACTIONp_mcangle_it2.5352
X-RAY DIFFRACTIONp_scbond_it5.7293.5
X-RAY DIFFRACTIONp_scangle_it8.4665
X-RAY DIFFRACTIONp_plane_restr0.0170.016
X-RAY DIFFRACTIONp_chiral_restr0.2080.13
X-RAY DIFFRACTIONp_singtor_nbd0.2790.35
X-RAY DIFFRACTIONp_multtor_nbd0.130.35
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1770.35
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.12.5
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 1 / Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 20046 / Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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