5D78 | pdb_00005d78

Structure of RRM3 Domain of Mip6 at 1.25 A Resolution

PDB DOI: https://doi.org/10.2210/pdb5D78/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-13 Released: 2016-08-17
Deposition Author(s): Mohamad, N., Bravo, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.177 (Depositor), 0.176 (DCC)
R-Value Work:
0.137 (Depositor), 0.138 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5D78

This is version 1.1 of the entry. See complete history.

Literature

Structure of RRM3 Domain of Mip6 at 1.25 A Resolution

Mohamad, N., Bravo, J.

To be published.

Macromolecule Content

Total Structure Weight: 9.36 kDa
Atom Count: 752
Modeled Residue Count: 81
Deposited Residue Count: 81
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein MIP6	A	81	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MIP6, YHR015W
UniProt
Find proteins for P38760 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38760 Go to UniProtKB: P38760
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCY Query on OCY	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.177 (Depositor), 0.176 (DCC)
R-Value Work: 0.137 (Depositor), 0.138 (DCC)
R-Value Observed: 0.139 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.842	α = 90
b = 47.023	β = 109.79
c = 30.563	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.