2EQA | pdb_00002eqa

Crystal Structure of the hypothetical Sua5 protein from Sulfolobus tokodaii

PDB DOI: https://doi.org/10.2210/pdb2EQA/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Sulfurisphaera tokodaii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-30 Released: 2008-01-15
Deposition Author(s): Agari, Y., Shinkai, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.208 (Depositor), 0.200 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4E1B

Literature

X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7

Agari, Y., Sato, S., Wakamatsu, T., Bessho, Y., Ebihara, A., Yokoyama, S., Kuramitsu, S., Shinkai, A.

(2008) Proteins 70: 1108-1111

PubMed: 18004774 Search on PubMed
DOI: https://doi.org/10.1002/prot.21794
Primary Citation of Related Structures:
2EQA

Organizational Affiliation

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Macromolecule Content

Total Structure Weight: 39.45 kDa
Atom Count: 2,768
Modelled Residue Count: 330
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ST1526	A	352	Sulfurisphaera tokodaii	Mutation(s): 0 Gene Names: SUA5 EC: 2.7.7.87
UniProt
Find proteins for Q970S6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970S6 Go to UniProtKB: Q970S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q970S6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.208 (Depositor), 0.200 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.391	α = 90
b = 120.843	β = 90
c = 67.552	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-15

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-01-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-11-20
Changes: Structure summary