3EXC | pdb_00003exc

Structure of the RNA'se SSO8090 from Sulfolobus solfataricus

PDB DOI: https://doi.org/10.2210/pdb3EXC/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-10-16 Released: 2008-11-11
Deposition Author(s): Singer, A.U., Skarina, T., Tan, K., Kagan, O., Onopriyenko, O., Edwards, A.M., Joachimiak, A., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.221 (Depositor), 0.275 (DCC)
R-Value Work:
0.191 (Depositor), 0.231 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3EXC

This is version 1.5 of the entry. See complete history.

Literature

Structure of the RNA'se SSO8090 from Sulfolobus solfataricus

Proudfoot, M., Brown, M., Singer, A.U., Skarina, T., Tan, K., Kagan, O., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F.

To be published.

Macromolecule Content

Total Structure Weight: 10.82 kDa
Atom Count: 685
Modeled Residue Count: 78
Deposited Residue Count: 91
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A [auth X]	91	Saccharolobus solfataricus	Mutation(s): 2 Gene Names: SSO8090 EC: 3.1.26 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for Q97Y85 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97Y85 Go to UniProtKB: Q97Y85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97Y85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A [auth X]	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.221 (Depositor), 0.275 (DCC)
R-Value Work: 0.191 (Depositor), 0.231 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.479	α = 90
b = 93.479	β = 90
c = 48.596	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-11

Deposition Author(s):

Onopriyenko, O.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-11-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-12-27
Changes: Data collection
Version 1.5: 2024-11-20
Changes: Structure summary