3K69 | pdb_00003k69

CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR (LP_0360) FROM LACTOBACILLUS PLANTARUM AT 1.95 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3K69/pdb

Classification: TRANSCRIPTION
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-08 Released: 2009-11-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.218 (Depositor), 0.222 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3K69

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

Literature

Crystal structure of Putative transcriptional regulator (NP_784167.1) from LACTOBACILLUS PLANTARUM at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 18.36 kDa
Atom Count: 1,354
Modeled Residue Count: 151
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcription regulator	A	162	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: lp_0360

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.218 (Depositor), 0.222 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.173	α = 90
b = 38.054	β = 110.73
c = 42.275	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Structure summary

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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.