4KR8 | pdb_00004kr8

Salmonella typhi OmpF complex with Daunomycin

PDB DOI: https://doi.org/10.2210/pdb4KR8/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhi
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2013-05-16 Released: 2014-05-28
Deposition Author(s): Madhuranayaki, T., Balasubramaniam, D., Krishnaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.366 (Depositor), 0.362 (DCC)
R-Value Work:
0.293 (Depositor), 0.293 (DCC)
R-Value Observed:
0.297 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Salmonella typhi OmpF complex with Daunomycin

Madhuranayaki, T., Balasubramaniam, D., Krishnaswamy, S.

To be published.

Macromolecule Content

Total Structure Weight: 114.19 kDa
Atom Count: 7,769
Modeled Residue Count: 1,020
Deposited Residue Count: 1,023
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein F	A, B, C	341	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0 Gene Names: ompF Membrane Entity: Yes
UniProt
Find proteins for P37432 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P37432 Go to UniProtKB: P37432
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37432
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DM1 Query on DM1 Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	DAUNOMYCIN C₂₇ H₂₉ N O₁₀ STQGQHZAVUOBTE-VGBVRHCVSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.366 (Depositor), 0.362 (DCC)
R-Value Work: 0.293 (Depositor), 0.293 (DCC)
R-Value Observed: 0.297 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.714	α = 90
b = 132.39	β = 90
c = 150.022	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Madhuranayaki, T.

Balasubramaniam, D.

Krishnaswamy, S.

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-11-08
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.