5SBJ

The crystal structure of METP in complex with Cd at a resolution of 1.29 A.

PDB DOI: https://doi.org/10.2210/pdb5SBJ/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., Pavone, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.170
R-Value Work: 0.151
R-Value Observed: 0.152

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

This is version 1.2 of the entry. See complete history.

Literature

Miniaturization process reloaded - structural and functional insights from a miniaturized rubredoxin

Chino, M., Di Costanzo, L.

To be published.

Macromolecule Content

Total Structure Weight: 3.07 kDa
Atom Count: 230
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

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 B [auth C] MOL2 format, chain B [auth C] mmCIF format, chain B [auth C]	B [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-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: 1.28 Å
R-Value Free: 0.170
R-Value Work: 0.151
R-Value Observed: 0.152
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.07	α = 90
b = 56.654	β = 90
c = 19.331	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Di Costanzo, L.

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection
Version 1.2: 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.