6Y5T

Crystal structure of savinase at room temperature

PDB DOI: https://doi.org/10.2210/pdb6Y5T/pdb

Classification: HYDROLASE
Organism(s): Lederbergia lenta
Expression System: Bacillus licheniformis
Mutation(s): No

Deposited: 2020-02-25 Released: 2020-06-17
Deposition Author(s): Wu, S., Moroz, O., Turkenburg, J., Nielsen, J.E., Wilson, K.S., Teilum, K.
Funding Organization(s): Danish Council for Independent Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.150
R-Value Work: 0.130
R-Value Observed: 0.131

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.

Wu, S., Nguyen, T.T.T.N., Moroz, O.V., Turkenburg, J.P., Nielsen, J.E., Wilson, K.S., Rand, K.D., Teilum, K.

(2020) PeerJ 8: e9408-e9408

PubMed: 32617193 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7717/peerj.9408
Primary Citation of Related Structures:
6Y5S, 6Y5T

PubMed Abstract:
Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown.

Organizational Affiliation

Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.

Macromolecule Content

Total Structure Weight: 26.78 kDa
Atom Count: 2,262
Modelled Residue Count: 269
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin Savinase	A	269	Lederbergia lenta	Mutation(s): 0 EC: 3.4.21.62
UniProt
Find proteins for P29600 (Lederbergia lenta) Explore P29600 Go to UniProtKB: P29600
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29600
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.150
R-Value Work: 0.130
R-Value Observed: 0.131
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.704	α = 90
b = 62.205	β = 90
c = 75.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	1335-00317B

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2020-07-15
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description