3KTS | pdb_00003kts

CRYSTAL STRUCTURE OF GLYCEROL UPTAKE OPERON ANTITERMINATOR REGULATORY PROTEIN FROM LISTERIA MONOCYTOGENES STR. 4b F2365

PDB DOI: https://doi.org/10.2210/pdb3KTS/pdb

Classification: TRANSCRIPTIONAL REGULATOR
Organism(s): Listeria monocytogenes serotype 4b str. F2365
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-25 Released: 2009-12-08
Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Do, J., 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: 2.75 Å
R-Value Free:
0.272 (Depositor), 0.273 (DCC)
R-Value Work:
0.218 (Depositor), 0.222 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KTS

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

Literature

CRYSTAL STRUCTURE OF GLYCEROL UPTAKE OPERON ANTITERMINATOR REGULATORY PROTEIN FROM LISTERIA MONOCYTOGENES STR. 4b F2365

Patskovsky, Y., Toro, R., Freeman, J., Do, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 170.37 kDa
Atom Count: 11,436
Modeled Residue Count: 1,474
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol uptake operon antiterminator regulatory protein	A, B, C, D, E A, B, C, D, E, F, G, H	192	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0 Gene Names: glpP, LMOf2365_1424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	Unknown ligand		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.272 (Depositor), 0.273 (DCC)
R-Value Work: 0.218 (Depositor), 0.222 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.603	α = 90
b = 110.599	β = 116.44
c = 130.971	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.