3RPD | pdb_00003rpd

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.

• PDB DOI: https://doi.org/10.2210/pdb3RPD/pdb

• Classification: TRANSFERASE
• Organism(s): Shewanella sp. W3-18-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-26 Released: 2011-08-31 
• Deposition Author(s): Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.189 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.

Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.95 kDa 
• Atom Count: 6,494 
• Modelled Residue Count: 686 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase (B12-independent)	A, B	357	Shewanella sp. W3-18-1	Mutation(s): 0  Gene Names: Sputw3181_1250 EC: 2.1.1.14

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MSE	D [auth A], G [auth B]	SELENOMETHIONINE C5 H11 N O2 Se RJFAYQIBOAGBLC-BYPYZUCNSA-N
GOL	E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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: 1.50 Å
• R-Value Free:  0.189 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.099	α = 90
b = 89.371	β = 92.45
c = 86.526	γ = 90

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: 2011-08-31 
Deposition Author(s): Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary