6D5N | pdb_00006d5n

Hexagonal thermolysin (295) in the presence of 50% xylose

  • Classification: HYDROLASE
  • Organism(s): Bacillus thermoproteolyticus
  • Mutation(s): No 

  • Deposited: 2018-04-19 Released: 2018-10-31 
  • Deposition Author(s): Juers, D.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.187 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6D5N

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.

Juers, D.H.Farley, C.A.Saxby, C.P.Cotter, R.A.Cahn, J.K.B.Holton-Burke, R.C.Harrison, K.Wu, Z.

(2018) Acta Crystallogr D Struct Biol 74: 922-938

  • DOI: https://doi.org/10.1107/S2059798318008793
  • Primary Citation Related Structures: 
    5UN3, 5UU7, 5UU8, 5UU9, 5UUA, 5UUB, 5UUC, 5UUD, 5UUE, 6AVL, 6B6N, 6B6O, 6B6P, 6B6Q, 6B6R, 6B6S, 6B6T, 6D5N, 6D5O, 6D5P, 6D5Q, 6D5R, 6D5S, 6D5T, 6D5U, 6D6E, 6D6F, 6D6G, 6D6H, 6DZF

  • PubMed Abstract: 

    Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.


  • Organizational Affiliation
    • Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA.

Macromolecule Content 

  • Total Structure Weight: 35.15 kDa 
  • Atom Count: 2,645 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYP

Query on XYP



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
LYS

Query on LYS



Download:Ideal Coordinates CCD File
C [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL

Query on VAL



Download:Ideal Coordinates CCD File
B [auth A]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.187 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.803α = 90
b = 93.803β = 90
c = 132.293γ = 120
Software Package:
Software NamePurpose
CrysalisProdata collection
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2018-10-31 
  • Deposition Author(s): Juers, D.H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R15GM090248

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Data collection, Database references, Structure summary