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- PDB-2sga: ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTUR... -

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Basic information

Entry
Database: PDB / ID: 2sga
TitleELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION
ComponentsPROTEINASE A
KeywordsHYDROLASE (SERINE PROTEINASE)
Function / homology
Function and homology information


streptogrisin A / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / 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: 1.5 Å
AuthorsJames, M.N.G. / Sielecki, A.R.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.
Authors: Moult, J. / Sussman, F. / James, M.N.
#1: Journal: J.Mol.Biol. / Year: 1980
Title: Structures of Product and Inhibitor Complexes of Streptomyces Griseus Protease a at 1.8 Angstroms Resolution. A Model for Serine Protease Catalysis
Authors: James, M.N.G. / Sielecki, A.R. / Brayer, G.D. / Delbaere, L.T.J. / Bauer, C.-A.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Protein Structure Refinement. Streptomyces Griseus Serine Protease a at 1.8 Angstroms Resolution
Authors: Sielecki, A.R. / Hendrickson, W.A. / Broughton, C.G. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
#3: Journal: J.Mol.Biol. / Year: 1980
Title: Structure of the Complex Formed between the Bacterial-Produced Inhibitor Chymostatin and the Serine Enzyme Streptomyces Griseus Protease A
Authors: Delbaere, L.T.J. / Brayer, G.D.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979
Title: Crystallographic and Kinetic Investigations of the Covalent Complex Formed by a Specific Tetrapeptide Aldehyde and the Serine Protease from Streptomyces Griseus
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G. / Bauer, C.-A. / Thompson, R.C.
#5: Journal: J.Mol.Biol. / Year: 1978
Title: Molecular Structure of Crystalline Streptomyces Griseus Protease a at 2.8 Angstroms Resolution. II. Molecular Conformation, Comparison with Alpha-Chymotrypsin and Active-Site Geometry
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
#6: Journal: J.Mol.Biol. / Year: 1978
Title: Molecular Structure of Crystalline Streptomyces Griseus Protease a at 2.8 Angstroms Resolution. I. Crystallization, Data Collection and Structural Analysis
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
#7: Journal: Can.J.Biochem. / Year: 1978
Title: Amino Acid Sequence Alignment of Bacterial and Mammalian Pancreatic Serine Proteases Based on Topological Equivalences
Authors: James, M.N.G. / Delbaere, L.T.J. / Brayer, G.D.
#8: Journal: Nature / Year: 1975
Title: Tertiary Structural Differences between Microbial Serine Proteases and Pancreatic Serine Enzymes
Authors: Delbaere, L.T.J. / Hutcheon, W.L.B. / James, M.N.G. / Thiessen, W.E.
History
DepositionJan 21, 1983-
SupersessionApr 21, 1983ID: 1SGA
Revision 1.0Apr 21, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE A


Theoretical massNumber of molelcules
Total (without water)18,0171
Polymers18,0171
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.120, 55.120, 54.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Atom site foot note1: THE SIDE CHAIN OF ARG 221 IS VERY DISORDERED. COORDINATES FOR THE ATOMS BEYOND CB HAVE BEEN OMITTED.
2: RESIDUE 99A IS A CIS-PROLINE.
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

21A-268-

HOH

31A-343-

HOH

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Components

#1: Protein PROTEINASE A


Mass: 18016.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / References: UniProt: P00776
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal grow
*PLUS
pH: 4.1 / Method: equilibrium dialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %(w/v)protein1reservoir
21.3 M1reservoirNaH2PO4

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.5→12 Å / Rfactor Rwork: 0.126
Details: THE WATER MOLECULES HAVE BEEN NUMBERED TO REFLECT THEIR ACCURACY, WITH HOH 1 BEING THE MOST ACCURATE. SOLVENT 1, ALTHOUGH REFINED AS WATER (OXYGEN ATOM), HAS BEEN INTERPRETED AS A NA+ ION. ...Details: THE WATER MOLECULES HAVE BEEN NUMBERED TO REFLECT THEIR ACCURACY, WITH HOH 1 BEING THE MOST ACCURATE. SOLVENT 1, ALTHOUGH REFINED AS WATER (OXYGEN ATOM), HAS BEEN INTERPRETED AS A NA+ ION. SEE REFERENCE 3 ABOVE FOR FURTHER DETAILS.
Refinement stepCycle: LAST / Resolution: 1.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 220 1479
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 19594 / σ(I): 2 / Rfactor obs: 0.121
Solvent computation
*PLUS
Displacement parameters
*PLUS

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