2DSL | pdb_00002dsl

Mutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2DSL/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-06-30 Released: 2006-12-30 
• Deposition Author(s): Shimizu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Mutant N33D structure of phenylacetic acid degradation protein PaaI from Thermus thermophilus HB8

Shimizu, K., Sugahara, M., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 28.62 kDa 
• Atom Count: 1,957 
• Modeled Residue Count: 230 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylacetic acid degradation protein PaaI	A, B	136	Thermus thermophilus HB8	Mutation(s): 1
UniProt
Find proteins for Q5SJP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJP3  Go to UniProtKB:  Q5SJP3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.67	α = 90
b = 57.67	β = 90
c = 139.696	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-30 
Deposition Author(s): Shimizu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-12-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description