8PRP | pdb_00008prp

The structure of nvBagel2 in the presence of Cd(II)

PDB DOI: https://doi.org/10.2210/pdb8PRP/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Dictyoglomus thermophilum H-6-12
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-07-12 Released: 2024-07-24
Deposition Author(s): Vandebroek, L., Voet, A.R.D., Lee, X.Y.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.313 (Depositor), 0.325 (DCC)
R-Value Work:
0.230 (Depositor), 0.234 (DCC)
R-Value Observed:
0.235 (Depositor)

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This is version 1.0 of the entry. See complete history.

Literature

The structure of nvBagel2 in the presence of Cd(II)

Vandebroek, L., Voet, A.R.D., Lee, X.Y.

To be published.

Macromolecule Content

Total Structure Weight: 9.28 kDa
Atom Count: 607
Modeled Residue Count: 79
Deposited Residue Count: 84
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell surface protein	A	84	Dictyoglomus thermophilum H-6-12	Mutation(s): 0 Gene Names: DICTH_0179
UniProt
Find proteins for B5YBJ6 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)) Explore B5YBJ6 Go to UniProtKB: B5YBJ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5YBJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.313 (Depositor), 0.325 (DCC)
R-Value Work: 0.230 (Depositor), 0.234 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.97	α = 90
b = 54.97	β = 90
c = 109.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1235722N

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

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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.