1MPT

CRYSTAL STRUCTURE OF A NEW ALKALINE SERINE PROTEASE (M-PROTEASE) FROM BACILLUS SP. KSM-K16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of a new alkaline serine protease (M-protease) from Bacillus sp. KSM-K16.

Yamane, T.Kani, T.Hatanaka, T.Suzuki, A.Ashida, T.Kobatashi, T.Ito, S.Yamashita, O.

(1995) Acta Crystallogr.,Sect.D 51: 199-206

  • DOI: 10.1107/S0907444994009960

  • PubMed Abstract: 
  • An alkaline serine protease, M-protease, from Bacillus sp. KSM-K16 has been crystallized. Two morphologically different crystal forms were obtained. Crystal data of form 1: space group P2(1)2(1)2(1), a = 47.3, b = 62.5, c = 75.6 A, V = 2.23 x 10(5) A ...

    An alkaline serine protease, M-protease, from Bacillus sp. KSM-K16 has been crystallized. Two morphologically different crystal forms were obtained. Crystal data of form 1: space group P2(1)2(1)2(1), a = 47.3, b = 62.5, c = 75.6 A, V = 2.23 x 10(5) A(3), Z = 4 and V(m) = 2.09 A(3) Da(-1). Crystal data of form 2: space group P2(1)2(1)2(1), a = 75.82 (2), b = 57.79 (2), c = 54.19 (1) A, V = 2.29 (2) x 10(5) A(3), Z = 4 and V(m) = 2.15 A(3) Da(-1). The crystal structure of M-protease in form 2 has been solved by molecular replacement using the atomic model of subtilisin Carlsberg (SBC) which is 60% homologous with M-protease, and refined to the crystallographic R-factor of 0.189 for 7004 reflections with F(o)/sigma(F) > 3 between 7 and 2.4 A resolution. The final model of M-protease contains 1882 protein atoms, two calcium ions and 44 water molecules. The three-dimensional structure of M-protease is essentially similar to other subtilisins of known structure. The 269 C(alpha) positions of M-protease have an r.m.s. difference of 1.06 A with the corresponding positions of SBC. The crystal data of form 2 are close to those of SBC, though the structure determination of form 2 made it clear that it is not isomorphous to the crystal structure of SBC. The deletions of amino acids occur at the residues 36' and 160'-163' compared with SBC (numerals with primes show the numbering for SBC). The deletion of the four residues (160'-163') may significantly affect the lack of isomorphism between M-protease and SBC.


    Organizational Affiliation

    Department of Biotechnology, School of Engineering, Nagoya University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M-PROTEASE
A
269Bacillus clausii (strain KSM-K16)Mutation(s): 0 
Gene Names: aprE
EC: 3.4.21.-
Find proteins for Q99405 (Bacillus clausii (strain KSM-K16))
Go to UniProtKB:  Q99405
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.820α = 90.00
b = 57.790β = 90.00
c = 54.190γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other
  • Version 1.4: 2019-07-17
    Type: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Type: Data collection, Refinement description