7QJN | pdb_00007qjn

Crystal structure of an alpha/beta-hydrolase enzyme from Candidatus Kryptobacter tengchongensis (306)

PDB DOI: https://doi.org/10.2210/pdb7QJN/pdb

Classification: HYDROLASE
Organism(s): Candidatus Kryptobacter tengchongensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-17 Released: 2022-12-28
Deposition Author(s): Zahn, M., Gill, R.S., Erickson, E., Beckham, G.T., McGeehan, J.E.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.250 (Depositor), 0.241 (DCC)
R-Value Work:
0.204 (Depositor), 0.195 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity

Erickson, E., Gado, J.E., Avilan, L., Bratti, F., Brizendine, R.K., Cox, P.A., Gill, R., Graham, R., Kim, D.J., Konig, G., Michener, W.E., Poudel, S., Ramirez, K.J., Shakespeare, T.J., Zahn, M., Boyd, E.S., Payne, C.M., DuBois, J.L., Pickford, A.R., Beckham, G.T., McGeehan, J.E.

(2022) Nat Commun 13: 7850

DOI: https://doi.org/10.1038/s41467-022-35237-x

Macromolecule Content

Total Structure Weight: 33.42 kDa
Atom Count: 2,339
Modeled Residue Count: 276
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dienelactone hydrolase	A	291	Candidatus Kryptobacter tengchongensis	Mutation(s): 0 Gene Names: JGI24_00892
UniProt
Find proteins for A0A656D8B6 (Kryptobacter tengchongensis) Explore A0A656D8B6 Go to UniProtKB: A0A656D8B6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A656D8B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.250 (Depositor), 0.241 (DCC)
R-Value Work: 0.204 (Depositor), 0.195 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.92	α = 90
b = 74.92	β = 90
c = 116.515	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	Research England E3 funding

Revision History (Full details and data files)

Version 1.0: 2022-12-28
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.