4KQD | pdb_00004kqd

The crystal Structure of the N-terminal PAS domain of the F plasmid TraJ

PDB DOI: https://doi.org/10.2210/pdb4KQD/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-14 Released: 2014-07-02
Deposition Author(s): Lu, J., Glover, J.N.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.178 (Depositor), 0.185 (DCC)
R-Value Work:
0.160 (Depositor), 0.171 (DCC)
R-Value Observed:
0.161 (Depositor)

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Ligand Structure Quality Assessment

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Literature

The crystal Structure of the N-terminal PAS domain of the F plasmid TraJ

Lu, J., Glover, J.N.M.

To be published.

Macromolecule Content

Total Structure Weight: 58.03 kDa
Atom Count: 4,274
Modeled Residue Count: 454
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein TraJ	A, B, C, D	121	Escherichia coli K-12	Mutation(s): 0 Gene Names: ECOK12F072, traJ
UniProt
Find proteins for P06626 (Escherichia coli (strain K12)) Explore P06626 Go to UniProtKB: P06626
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06626
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTT Query on DTT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DTD Query on DTD Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	F [auth B], H [auth D]	DITHIANE DIOL C₄ H₈ O₂ S₂ YPGMOWHXEQDBBV-IMJSIDKUSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.178 (Depositor), 0.185 (DCC)
R-Value Work: 0.160 (Depositor), 0.171 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.228	α = 90
b = 95.228	β = 90
c = 102.041	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.