3DCL | pdb_00003dcl

Crystal structure of TM1086

• PDB DOI: https://doi.org/10.2210/pdb3DCL/pdb

• Classification: structural genomics, unknown function
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-03 Released: 2008-08-05 
• Deposition Author(s): Chruszcz, M., Evdokimova, E., Kudritska, M., 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: 2.25 Å
• R-Value Free: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal structure of TM1086

Chruszcz, M., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 155.93 kDa 
• Atom Count: 11,271 
• Modeled Residue Count: 1,408 
• Deposited Residue Count: 1,420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TM1086	A, B, C, D, E	284	Thermotoga maritima	Mutation(s): 0  Gene Names: TM_1086
UniProt
Find proteins for Q9X0H2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0H2  Go to UniProtKB:  Q9X0H2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth D], BA [auth D], F [auth A], FA [auth E], G [auth A], GA [auth E], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], Z [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	EA [auth D], JA [auth E], L [auth A], S [auth B], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	CA [auth D], DA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], K [auth A], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C, D, E	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.578	α = 90
b = 164.578	β = 90
c = 97.815	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
MAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Chruszcz, M., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2011-10-05
  Changes: Structure summary
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary