5O8N | pdb_00005o8n

Structure of thermolysin at room temperature via a method of acoustically induced rotation.

PDB DOI: https://doi.org/10.2210/pdb5O8N/pdb

Classification: HYDROLASE
Organism(s): Bacillus thermoproteolyticus
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-06-13 Released: 2017-08-09
Deposition Author(s): Axford, D.N., Burton, C., Docker, P., Prince, M., Topham, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.200 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

An acoustic on-chip goniometer for room temperature macromolecular crystallography.

Burton, C.G., Axford, D., Edwards, A.M.J., Gildea, R.J., Morris, R.H., Newton, M.I., Orville, A.M., Prince, M., Topham, P.D., Docker, P.T.

(2017) Lab Chip 17: 4225-4230

PubMed: 29124258 Search on PubMed
DOI: https://doi.org/10.1039/c7lc00812k
Primary Citation Related Structures:
5O8N

PubMed Abstract:
This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

Organizational Affiliation

Aston Institute of Material Research, Aston University, Birmingham B4 7ET, UK.

Macromolecule Content

Total Structure Weight: 34.81 kDa
Atom Count: 2,593
Modeled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0 Gene Names: npr EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800 Go to UniProtKB: P00800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00800
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], M [auth A], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain M [auth A] Focus chain N [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.200 (Depositor), 0.202 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.552	α = 90
b = 93.552	β = 90
c = 129.753	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
cctbx.prime	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-08-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-09
Type: Initial release
Version 1.1: 2017-11-22
Changes: Database references
Version 1.2: 2017-12-13
Changes: Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description