4BS9 | pdb_00004bs9

Structure of the heterocyclase TruD

PDB DOI: https://doi.org/10.2210/pdb4BS9/pdb

Classification: ISOMERASE
Organism(s): uncultured Prochloron sp. 06037A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-06-09 Released: 2013-11-06
Deposition Author(s): Koehnke, J., Bent, A.F., Zollman, D., Smith, K., Houssen, W.E., Zhu, X., Mann, G., Lebl, T., Scharff, R., Shirran, S., Botting, C.H., Jaspars, M., Schwarz-Linek, U., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.237 (Depositor)
R-Value Work:
0.185 (Depositor), 0.195 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase that Operates with a Defined Order of Reaction.

Koehnke, J., Bent, A.F., Zollman, D., Smith, K., Houssen, W.E., Zhu, X., Mann, G., Lebl, T., Scharff, R., Shirran, S., Botting, C.H., Jaspars, M., Schwarz-Linek, U., Naismith, J.H.

(2013) Angew Chem Int Ed Engl 52: 13991

PubMed: 24214017 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.201306302
Primary Citation Related Structures:
4BS9

Organizational Affiliation

Biomedical Science Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST (UK).

Macromolecule Content

Total Structure Weight: 87.2 kDa
Atom Count: 5,472
Modeled Residue Count: 691
Deposited Residue Count: 781
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRUD	A	781	uncultured Prochloron sp. 06037A	Mutation(s): 0
UniProt
Find proteins for B2KYG8 (uncultured Prochloron sp. 06037A) Explore B2KYG8 Go to UniProtKB: B2KYG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2KYG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.237 (Depositor)
R-Value Work: 0.185 (Depositor), 0.195 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.27	α = 90
b = 138.27	β = 90
c = 280.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 1.1: 2013-11-20
Changes: Database references
Version 1.2: 2014-01-08
Changes: Database references
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other