3DPJ | pdb_00003dpj

The crystal structure of a TetR transcription regulator from Silicibacter pomeroyi DSS

PDB DOI: https://doi.org/10.2210/pdb3DPJ/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Ruegeria pomeroyi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-08 Released: 2008-09-02
Deposition Author(s): Tan, K., Li, H., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.243 (Depositor), 0.199 (DCC)
R-Value Work:
0.193 (Depositor), 0.177 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a TetR transcription regulator from Silicibacter pomeroyi DSS

Tan, K., Li, H., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 178.77 kDa
Atom Count: 12,978
Modeled Residue Count: 1,530
Deposited Residue Count: 1,552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulator, TetR family	A, B, C, D, E A, B, C, D, E, F, G, H	194	Ruegeria pomeroyi	Mutation(s): 0 Gene Names: SPO1902
UniProt
Find proteins for Q5LS67 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LS67 Go to UniProtKB: Q5LS67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LS67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain LA [auth G] SDF format, chain MA [auth H] SDF format, chain O [auth C] SDF format, chain W [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain O [auth C] MOL2 format, chain W [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain O [auth C] mmCIF format, chain W [auth D]	CA [auth E] GA [auth F] I [auth A] K [auth B] LA [auth G] CA [auth E], GA [auth F], I [auth A], K [auth B], LA [auth G], MA [auth H], O [auth C], W [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain K [auth B] Focus chain LA [auth G] Focus chain MA [auth H] Focus chain O [auth C] Focus chain W [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain K [auth B] Focus chain LA [auth G] Focus chain MA [auth H] Focus chain O [auth C] Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain NA [auth H] SDF format, chain OA [auth H] SDF format, chain P [auth C] SDF format, chain PA [auth H] SDF format, chain Q [auth C] SDF format, chain QA [auth H] SDF format, chain R [auth C] SDF format, chain RA [auth H] SDF format, chain S [auth C] SDF format, chain SA [auth H] SDF format, chain T [auth C] SDF format, chain TA [auth H] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth H] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth C] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth H] mmCIF format, chain OA [auth H] mmCIF format, chain P [auth C] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain QA [auth H] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] DA [auth E] EA [auth E] FA [auth E] AA [auth D], BA [auth D], DA [auth E], EA [auth E], FA [auth E], HA [auth F], IA [auth F], J [auth A], JA [auth F], KA [auth F], L [auth B], M [auth B], N [auth B], NA [auth H], OA [auth H], P [auth C], PA [auth H], Q [auth C], QA [auth H], R [auth C], RA [auth H], S [auth C], SA [auth H], T [auth C], TA [auth H], U [auth C], V [auth C], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain P [auth C] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain QA [auth H] Focus chain R [auth C] Focus chain RA [auth H] Focus chain S [auth C] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain P [auth C] Focus chain PA [auth H] Focus chain Q [auth C] Focus chain QA [auth H] Focus chain R [auth C] Focus chain RA [auth H] Focus chain S [auth C] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [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, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243 (Depositor), 0.199 (DCC)
R-Value Work: 0.193 (Depositor), 0.177 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.523	α = 89.35
b = 93.072	β = 71.02
c = 93.397	γ = 71.04

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary