3QTD | pdb_00003qtd

Crystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1

• PDB DOI: https://doi.org/10.2210/pdb3QTD/pdb

• Classification: GENE REGULATION
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-22 Released: 2011-03-30 
• Deposition Author(s): Tkaczuk, K.L., Chruszcz, M., Evdokimova, E., Liu, F., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.279 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1

Tkaczuk, K.L., Chruszcz, M., Evdokimova, E., Liu, F., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 194.18 kDa 
• Atom Count: 13,604 
• Modeled Residue Count: 1,766 
• Deposited Residue Count: 1,796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PmbA protein	A, B, C, D	449	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA4472, pmbA, PmbA_TldD
UniProt
Find proteins for Q9HVU9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVU9  Go to UniProtKB:  Q9HVU9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.279 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.385	α = 90
b = 116.201	β = 90
c = 253.968	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXE	model building
DM	model building
MLPHARE	phasing
RESOLVE	model building
CCP4	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-30 
Deposition Author(s): Tkaczuk, K.L., Chruszcz, M., Evdokimova, E., Liu, F., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary