5SBG | pdb_00005sbg

The crystal structure of METP in complex with Zn at a resolution of 1.34 A.

PDB DOI: https://doi.org/10.2210/pdb5SBG/pdb
Deposition Group: G_1002191 ExploreG_1002191

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2021-08-24 Released: 2023-02-15
Deposition Author(s): Di Costanzo, L., La Gatta, S., Chino, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.174 (Depositor), 0.170 (DCC)
R-Value Work:
0.131 (Depositor), 0.130 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light

Chino, M., Di Costanzo, L.F., Leone, L., La Gatta, S., Famulari, A., Chiesa, M., Lombardi, A., Pavone, V.

(2023) Nat Commun 14: 2368

DOI: https://doi.org/10.1038/s41467-023-37941-8

Macromolecule Content

Total Structure Weight: 3.02 kDa
Atom Count: 238
Modelled Residue Count: 30
Deposited Residue Count: 30
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METP, miniaturized rubredoxin	A [auth C]	30	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	A [auth C]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.174 (Depositor), 0.170 (DCC)
R-Value Work: 0.131 (Depositor), 0.130 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.663	α = 90
b = 55.978	β = 90
c = 19.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Di Costanzo, L.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2023-05-17
Changes: Database references
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-04-03
Changes: Refinement description

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.