3M4R | pdb_00003m4r

Structure of the N-terminal Class II Aldolase domain of a conserved protein from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb3M4R/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-11 Released: 2010-04-14 
• Deposition Author(s): Cuff, M.E., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Structure of the N-terminal Class II Aldolase domain of a conserved protein from Thermoplasma acidophilum

Cuff, M.E., Li, H., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 24.84 kDa 
• Atom Count: 1,804 
• Modeled Residue Count: 213 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	222	Thermoplasma acidophilum	Mutation(s): 0  Gene Names: PRK08324, Ta0481
UniProt
Find proteins for Q9HKW2 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKW2  Go to UniProtKB:  Q9HKW2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.136	α = 90
b = 46.136	β = 90
c = 203.998	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Cuff, M.E., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary