6JPI | pdb_00006jpi

Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb6JPI/pdb
NAKB: 6JPI

Classification: ANTITOXIN/DNA
Organism(s): Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-03-27 Released: 2020-04-01
Deposition Author(s): Liu, Y., Gao, Z., Zhang, H., Dong, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free:
0.281 (Depositor), 0.282 (DCC)
R-Value Work:
0.215 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa

Liu, Y., Gao, Z., Zhang, H., Dong, Y.

To be published.

Macromolecule Content

Total Structure Weight: 66.14 kDa
Atom Count: 4,073
Modeled Residue Count: 425
Deposited Residue Count: 492
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH cro/C1-type domain-containing protein	A, B, C, D	109	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA4674
UniProt
Find proteins for Q9HVC1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVC1 Go to UniProtKB: Q9HVC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HVC1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (28-MER)	E	28	Pseudomonas aeruginosa
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (28-MER)	F	28	Pseudomonas aeruginosa
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free: 0.281 (Depositor), 0.282 (DCC)
R-Value Work: 0.215 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.8	α = 90
b = 90.7	β = 90
c = 91.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	U1732113

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, 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.