3NJH | pdb_00003njh

D37A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.

PDB DOI: https://doi.org/10.2210/pdb3NJH/pdb

Classification: HYDROLASE
Organism(s): Shewanella oneidensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-06-17 Released: 2010-07-14
Deposition Author(s): Osipiuk, J., Mulligan, R., Bargassa, M., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.152 (Depositor), 0.159 (DCC)
R-Value Work:
0.127 (Depositor), 0.140 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.

Osipiuk, J., Mulligan, R., Bargassa, M., Hamilton, J.E., Cunningham, M.A., Joachimiak, A.

(2012) J Biological Chem 287: 19452-19461

PubMed: 22493430 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.358069
Primary Citation Related Structures:
3N55, 3NJF, 3NJG, 3NJH, 3NJI, 3NJJ, 3NJK, 3NJL, 3NJM, 3NJN

PubMed Abstract:
The crystal structure of SO1698 protein from Shewanella oneidensis was determined by a SAD method and refined to 1.57 Å. The structure is a β sandwich that unexpectedly consists of two polypeptides; the N-terminal fragment includes residues 1-116, and the C-terminal one includes residues 117-125. Electron density also displayed the Lys-98 side chain covalently linked to Asp-116. The putative active site residues involved in self-cleavage were identified; point mutants were produced and characterized structurally and in a biochemical assay. Numerical simulations utilizing molecular dynamics and hybrid quantum/classical calculations suggest a mechanism involving activation of a water molecule coordinated by a catalytic aspartic acid.

Organizational Affiliation

Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecule Content

Total Structure Weight: 55.03 kDa
Atom Count: 4,040
Modeled Residue Count: 484
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase	A, B, C, D	128	Shewanella oneidensis	Mutation(s): 1 Gene Names: SO_1698
UniProt
Find proteins for Q8EGA7 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EGA7 Go to UniProtKB: Q8EGA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EGA7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], J [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.152 (Depositor), 0.159 (DCC)
R-Value Work: 0.127 (Depositor), 0.140 (DCC)
R-Value Observed: 0.130 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.986	α = 90
b = 97.986	β = 90
c = 65.844	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-10-10
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description