1O5H | pdb_00001o5h

Crystal structure of formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O5H/pdb

• Classification: LYASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-09-17 Released: 2003-09-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold

Xu, Q., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Biorac, T., Canaves, J.M., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hampton, E., Hornsby, M., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Quijano, K., Reyes, R., Robb, A., Sims, E., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., von Delft, F., Wang, X., West, B., White, A., Wolf, G., Zagnitko, O., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2005) Proteins 58: 976-981

• PubMed: 15651027 
• DOI: https://doi.org/10.1002/prot.20364
• Primary Citation of Related Structures:  
  1O5H

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Organizational Affiliation: 
• The Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA.

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)

Macromolecule Content 

• Total Structure Weight: 49.63 kDa 
• Atom Count: 3,051 
• Modeled Residue Count: 398 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formiminotetrahydrofolate cyclodeaminase	A, B	214	Thermotoga maritima	Mutation(s): 12  Gene Names: TM1560 EC: 4.3.1.4
UniProt
Find proteins for Q9X1P6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1P6  Go to UniProtKB:  Q9X1P6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O5H

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.704	α = 90
b = 71.875	β = 90
c = 119.245	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection, Database references
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary