1U3F

Structural and Functional Characterization of a 5,10-Methenyltetrahydrofolate Synthetase from Mycoplasma pneumoniae (GI: 13508087)

• PDB DOI: https://doi.org/10.2210/pdb1U3F/pdb

• Classification: LIGASE
• Organism(s): Mycoplasmoides pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-21 Released: 2004-12-07 
• Deposition Author(s): Chen, S., Yakunin, A.F., Proudfoot, M., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution

Chen, S., Shin, D.H., Pufan, R., Kim, R., Kim, S.-H.

(2004) Proteins 56: 839-843

• PubMed: 15281135 
• DOI: https://doi.org/10.1002/prot.20214
• Primary Citation of Related Structures:  
  1SBQ, 1U3F, 1U3G

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley, California.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.64 kDa 
• Atom Count: 3,033 
• Modelled Residue Count: 328 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-Methenyltetrahydrofolate Synthetase	A, B	189	Mycoplasmoides pneumoniae	Mutation(s): 0  EC: 6.3.3.2
UniProt
Find proteins for P75430 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75430  Go to UniProtKB:  P75430

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.135	α = 90
b = 74.369	β = 90
c = 110.614	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-07 
Deposition Author(s): Chen, S., Yakunin, A.F., Proudfoot, M., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2004-12-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Structure summary