3EEY | pdb_00003eey

CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium thermocellum

PDB DOI: https://doi.org/10.2210/pdb3EEY/pdb

Classification: TRANSFERASE
Organism(s): Acetivibrio thermocellus ATCC 27405
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-06 Released: 2008-09-16
Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Rutter, M., Hu, S., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.278 (Depositor), 0.266 (DCC)
R-Value Work:
0.244 (Depositor), 0.237 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Rrna-Methylase from Clostridium Thermocellum

Patskovsky, Y., Ramagopal, U.A., Toro, R., Rutter, M., Hu, S., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 222.81 kDa
Atom Count: 15,399
Modeled Residue Count: 1,887
Deposited Residue Count: 1,970
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative rRNA methylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	197	Acetivibrio thermocellus ATCC 27405	Mutation(s): 0 Gene Names: Cthe_0696
UniProt
Find proteins for A3DDA2 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DDA2 Go to UniProtKB: A3DDA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3DDA2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain S [auth C] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth H] SDF format, chain U [auth D] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain BA [auth J] MOL2 format, chain AA [auth I] MOL2 format, chain S [auth C] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth H] MOL2 format, chain U [auth D] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain BA [auth J] mmCIF format, chain AA [auth I] mmCIF format, chain S [auth C] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth H] mmCIF format, chain U [auth D] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain BA [auth J]	AA [auth I] BA [auth J] K [auth A] P [auth B] S [auth C] AA [auth I], BA [auth J], K [auth A], P [auth B], S [auth C], U [auth D], V [auth E], W [auth F], Y [auth H]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain K [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain K [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain Y [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A], N [auth A], Q [auth B], T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Z [auth H] SDF format, chain X [auth F] SDF format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth F] MOL2 format, chain R [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth F] mmCIF format, chain R [auth B]	O [auth A], R [auth B], X [auth F], Z [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain R [auth B] Focus chain X [auth F] Focus chain Z [auth H] Interactions & Density Focus chain O [auth A] Focus chain R [auth B] Focus chain X [auth F] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.278 (Depositor), 0.266 (DCC)
R-Value Work: 0.244 (Depositor), 0.237 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.156	α = 90
b = 126.913	β = 99.54
c = 125.611	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2018-11-14
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Refinement description