3MD1 | pdb_00003md1

Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)

PDB DOI: https://doi.org/10.2210/pdb3MD1/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2010-03-29 Released: 2010-05-05
Deposition Author(s): Li, H., Shi, H., Li, Y., Cui, Y., Niu, L., Teng, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.221 (Depositor), 0.270 (DCC)
R-Value Work:
0.198 (Depositor)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)

Li, H., Shi, H., Li, Y., Cui, Y., Niu, L., Teng, M.

To be published.

Macromolecule Content

Total Structure Weight: 18.95 kDa
Atom Count: 1,472
Modeled Residue Count: 162
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1	A, B	83	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32588 Go to UniProtKB: P32588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32588
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.221 (Depositor), 0.270 (DCC)
R-Value Work: 0.198 (Depositor)
R-Value Observed: 0.199 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.661	α = 90
b = 72.661	β = 90
c = 81.989	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.