4LZL | pdb_00004lzl

Structure of the inactive form of the regulatory domain from the repressor of iron transport regulator (RitR)

PDB DOI: https://doi.org/10.2210/pdb4LZL/pdb

Classification: TRANSCRIPTION
Organism(s): Streptococcus pneumoniae 2061617
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-31 Released: 2014-09-17
Deposition Author(s): Silvaggi, N.R., Han, L., Ulijasz, A.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.161 (Depositor), 0.157 (DCC)
R-Value Work:
0.141 (Depositor), 0.140 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Defining the Aspartate-Less Receiver (ALR) Domains: Structure and Activation of RitR from Streptococcus pneumoniae

Maule, A.F., Weiner, J.J., Han, L., Wright, D.P., Peterson, F.C., Volkman, B.F., Silvaggi, N.R., Ulijasz, A.T.

To be published.

Macromolecule Content

Total Structure Weight: 14.56 kDa
Atom Count: 1,300
Modeled Residue Count: 123
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator	A	124	Streptococcus pneumoniae 2061617	Mutation(s): 0 Gene Names: AMCSP02_000425, RitR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.161 (Depositor), 0.157 (DCC)
R-Value Work: 0.141 (Depositor), 0.140 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.46	α = 92.65
b = 33.84	β = 103.71
c = 34.96	γ = 97.53

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.