- PDB-1mpt: CRYSTAL STRUCTURE OF A NEW ALKALINE SERINE PROTEASE (M-PROTEASE) ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1mpt
Title
CRYSTAL STRUCTURE OF A NEW ALKALINE SERINE PROTEASE (M-PROTEASE) FROM BACILLUS SP. KSM-K16
Components
M-PROTEASE
Keywords
SERINE PROTEINASE
Function / homology
Function and homology information
Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function
1: CIS PROLINE - PRO 168 2: THE O ATOM OF SER 221, WHICH IS CONTAINED IN THE ACTIVE SITES, WAS MODIFIED WITH PHENYLMETHYLSULFONYLFLUORIDE (PMSF); HOWEVER, THE PMSF GROUP WAS NOT CONSTRUCTED DUE TO THE LACK OF ELECTRON DENSITY.
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Components
#1: Protein
M-PROTEASE
Mass: 26743.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus clausii (bacteria) / Strain: KSM-K16 / References: UniProt: Q99405, subtilisin
Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Compound details
THE O ATOM OF SER 221, WHICH IS CONTAINED IN THE ACTIVE SITES, WAS MODIFIED WITH ...THE O ATOM OF SER 221, WHICH IS CONTAINED IN THE ACTIVE SITES, WAS MODIFIED WITH PHENYLMETHYLSULFONYLFLUORIDE (PMSF); HOWEVER, THE PMSF GROUP WAS NOT CONSTRUCTED DUE TO THE LACK OF ELECTRON DENSITY.
Sequence details
THE AMINO ACI SEQUENCE FOR THIS ENTRY IS FROM HAKAMADA, Y., KOBAYASHI, T., HITOMI, J., KAWAI, S. & ...THE AMINO ACI SEQUENCE FOR THIS ENTRY IS FROM HAKAMADA, Y., KOBAYASHI, T., HITOMI, J., KAWAI, S. & ITO, S. (1994) J. FERMET. BIOENG., ACCEPTED FOR PUBLICATION.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
ID
Conc.
Common name
Crystal-ID
Sol-ID
1
10mg/ml
enzyme
1
drop
2
50mM
acetate
1
drop
3
50mM
acetate
1
reservoir
4
1.4M
ammoniumsulphate
1
reservoir
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Data collection
Radiation
Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 100 Å / Num. obs: 7897 / % possible obs: 80.6 % / Num. measured all: 24185 / Rmerge(I) obs: 0.119
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Processing
Software
Name
Classification
X-PLOR
modelbuilding
PROLSQ
refinement
X-PLOR
refinement
X-PLOR
phasing
Refinement
Resolution: 2.4→7 Å / σ(F): 3 /
Rfactor
Num. reflection
Rwork
0.189
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obs
0.189
7004
Refinement step
Cycle: LAST / Resolution: 2.4→7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1882
0
2
44
1928
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.016
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
0.748
1
X-RAY DIFFRACTION
x_mcangle_it
1.222
1.5
X-RAY DIFFRACTION
x_scbond_it
0.825
1
X-RAY DIFFRACTION
x_scangle_it
1.309
1.5
Refinement
*PLUS
Rfactor obs: 0.189 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal target
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.02
X-RAY DIFFRACTION
x_angle_d
0.03
0.038
X-RAY DIFFRACTION
x_planar_d
0.04
0.047
X-RAY DIFFRACTION
x_plane_restr
0.02
0.014
X-RAY DIFFRACTION
x_chiral_restr
0.15
0.175
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