2C37

RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA

PDB DOI: https://doi.org/10.2210/pdb2C37/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-10-04 Released: 2005-11-23
Deposition Author(s): Lorentzen, E., Conti, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282
R-Value Work: 0.266
R-Value Observed: 0.267

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 702.87 kDa
Atom Count: 46,570
Modelled Residue Count: 6,044
Deposited Residue Count: 6,276
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	275	Saccharolobus solfataricus	Mutation(s): 0 EC: 3.1.13
UniProt
Find proteins for Q9UXC0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q9UXC0 Go to UniProtKB: Q9UXC0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UXC0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	248	Saccharolobus solfataricus	Mutation(s): 0 EC: 3.1.13
UniProt
Find proteins for Q9UXC2 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q9UXC2 Go to UniProtKB: Q9UXC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UXC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download Ideal Coordinates CCD File SDF format, chain AB [auth U] SDF format, chain BA [auth B] SDF format, chain BB [auth U] SDF format, chain CA [auth B] SDF format, chain CB [auth U] SDF format, chain EA [auth E] SDF format, chain EB [auth V] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain GB [auth W] SDF format, chain HB [auth W] SDF format, chain IA [auth F] SDF format, chain IB [auth W] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain KB [auth X] SDF format, chain MA [auth H] SDF format, chain NA [auth I] SDF format, chain OA [auth I] SDF format, chain QA [auth J] SDF format, chain SA [auth M] SDF format, chain TA [auth M] SDF format, chain VA [auth N] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AB [auth U] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth U] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth U] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth V] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth W] MOL2 format, chain HB [auth W] MOL2 format, chain IA [auth F] MOL2 format, chain IB [auth W] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain KB [auth X] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain QA [auth J] MOL2 format, chain SA [auth M] MOL2 format, chain TA [auth M] MOL2 format, chain VA [auth N] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	AB [auth U] BA [auth B] BB [auth U] CA [auth B] CB [auth U] AB [auth U], BA [auth B], BB [auth U], CA [auth B], CB [auth U], EA [auth E], EB [auth V], FA [auth E], GA [auth E], GB [auth W], HB [auth W], IA [auth F], IB [auth W], JA [auth G], KA [auth G], KB [auth X], MA [auth H], NA [auth I], OA [auth I], QA [auth J], SA [auth M], TA [auth M], VA [auth N], Y [auth A], Z [auth A]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain AB [auth U] Focus chain BA [auth B] Focus chain BB [auth U] Focus chain CA [auth B] Focus chain CB [auth U] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain GB [auth W] Focus chain HB [auth W] Focus chain IA [auth F] Focus chain IB [auth W] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain KB [auth X] Focus chain MA [auth H] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain SA [auth M] Focus chain TA [auth M] Focus chain VA [auth N] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth U] Focus chain BA [auth B] Focus chain BB [auth U] Focus chain CA [auth B] Focus chain CB [auth U] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain GB [auth W] Focus chain HB [auth W] Focus chain IA [auth F] Focus chain IB [auth W] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain KB [auth X] Focus chain MA [auth H] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain SA [auth M] Focus chain TA [auth M] Focus chain VA [auth N] Focus chain Y [auth A] Focus chain Z [auth A]
RP5 Query on RP5 Download Ideal Coordinates CCD File SDF format, chain WA [auth N] MOL2 format, chain WA [auth N]	WA [auth N]	5-O-phosphono-beta-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-TXICZTDVSA-N		Interactions Focus chain WA [auth N] Interactions & Density Focus chain WA [auth N]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain ZA [auth T] SDF format, chain AA [auth B] SDF format, chain DA [auth D] SDF format, chain DB [auth V] SDF format, chain HA [auth F] SDF format, chain JB [auth X] SDF format, chain LA [auth H] SDF format, chain PA [auth J] SDF format, chain RA [auth L] SDF format, chain UA [auth N] SDF format, chain XA [auth P] SDF format, chain YA [auth R] MOL2 format, chain ZA [auth T] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth V] MOL2 format, chain HA [auth F] MOL2 format, chain JB [auth X] MOL2 format, chain LA [auth H] MOL2 format, chain PA [auth J] MOL2 format, chain RA [auth L] MOL2 format, chain UA [auth N] MOL2 format, chain XA [auth P] MOL2 format, chain YA [auth R]	AA [auth B] DA [auth D] DB [auth V] HA [auth F] JB [auth X] AA [auth B], DA [auth D], DB [auth V], HA [auth F], JB [auth X], LA [auth H], PA [auth J], RA [auth L], UA [auth N], XA [auth P], YA [auth R], ZA [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain HA [auth F] Focus chain JB [auth X] Focus chain LA [auth H] Focus chain PA [auth J] Focus chain RA [auth L] Focus chain UA [auth N] Focus chain XA [auth P] Focus chain YA [auth R] Focus chain ZA [auth T] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain HA [auth F] Focus chain JB [auth X] Focus chain LA [auth H] Focus chain PA [auth J] Focus chain RA [auth L] Focus chain UA [auth N] Focus chain XA [auth P] Focus chain YA [auth R] Focus chain ZA [auth T]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FB [auth V] MOL2 format, chain FB [auth V]	FB [auth V]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FB [auth V] Interactions & Density Focus chain FB [auth V]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282
R-Value Work: 0.266
R-Value Observed: 0.267
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.02	α = 90
b = 212.94	β = 90
c = 433.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-11-23

Deposition Author(s):

Lorentzen, E.

Conti, E.

Revision History (Full details and data files)

Version 1.0: 2005-11-23
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary