2A2O

CRYSTAL STRUCTURE OF a putativeTenA family transcriptional regulator (BT_3146) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.16 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2A2O/pdb

Classification: TRANSCRIPTION
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-06-22 Released: 2005-07-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.173 (Depositor), 0.190 (DCC)
R-Value Work:
0.145 (Depositor), 0.160 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of (np_812058.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.16 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 212.1 kDa
Atom Count: 14,881
Modelled Residue Count: 1,608
Deposited Residue Count: 1,806
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 BT3146	A, B, C, D, E A, B, C, D, E, F, G	258	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 7 Gene Names: np_812058.1
UniProt
Find proteins for Q8A309 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A309 Go to UniProtKB: Q8A309
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A309
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain OA [auth G] SDF format, chain P [auth B] SDF format, chain PA [auth G] SDF format, chain QA [auth G] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	BA [auth E] CA [auth E] DA [auth E] EA [auth E] FA [auth E] BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth E], H [auth A], HA [auth F], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], NA [auth G], O [auth B], OA [auth G], P [auth B], PA [auth G], QA [auth G], R [auth C], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain GA [auth F] SDF format, chain M [auth B] SDF format, chain MA [auth G] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	AA [auth E] GA [auth F] M [auth B] MA [auth G] N [auth B] AA [auth E], GA [auth F], M [auth B], MA [auth G], N [auth B], Q [auth C], U [auth D], V [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain GA [auth F] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain GA [auth F] Focus chain M [auth B] Focus chain MA [auth G] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.173 (Depositor), 0.190 (DCC)
R-Value Work: 0.145 (Depositor), 0.160 (DCC)

Diffraction Data: https://doi.org/10.18430/M32A2O

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.238	α = 90
b = 201.238	β = 90
c = 291.03	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary