3LFR | pdb_00003lfr

The Crystal Structure of a CBS Domain from a Putative Metal Ion Transporter Bound to AMP from Pseudomonas syringae to 1.55A

• PDB DOI: https://doi.org/10.2210/pdb3LFR/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pseudomonas syringae pv. tomato str. DC3000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-18 Released: 2010-01-26 
• Deposition Author(s): Stein, A.J., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

The Crystal Structure of a CBS Domain from a Putative Metal Ion Transporter Bound to AMP from Pseudomonas syringae to 1.55A

Stein, A.J., Bigelow, L., Cobb, G., Joachimiak, A.

To be published.

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: 31.19 kDa 
• Atom Count: 2,171 
• Modeled Residue Count: 251 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Metal ion transporter	A, B	136	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0  Gene Names: PSPTO4807, PSPTO_4807
UniProt
Find proteins for Q87VX8 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87VX8  Go to UniProtKB:  Q87VX8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-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: 1.53 Å
• R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.15	α = 90
b = 50.65	β = 112.26
c = 51.867	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Stein, A.J., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary