4WED | pdb_00004wed

Crystal structure of ABC transporter substrate-binding protein from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb4WED/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-09 Released: 2014-09-24 
• Deposition Author(s): Shabalin, I.G., Otwinowski, Z., Bacal, P., Cymborowski, M.T., Handing, K.B., Stead, M., Hammonds, J., Ahmed, M., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of ABC transporter substrate-binding protein from Sinorhizobium meliloti

Shabalin, I.G., Handing, K.B., Minor, W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 58.19 kDa 
• Atom Count: 3,720 
• Modeled Residue Count: 483 
• Deposited Residue Count: 525 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, periplasmic solute-binding protein	A	525	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMa1651
UniProt
Find proteins for Q92YH7 (Rhizobium meliloti (strain 1021)) Explore Q92YH7  Go to UniProtKB:  Q92YH7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3KG69

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.327	α = 90
b = 57.327	β = 90
c = 132.063	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
DM	phasing
MLPHARE	phasing
SHELX	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Shabalin, I.G., Otwinowski, Z., Bacal, P., Cymborowski, M.T., Handing, K.B., Stead, M., Hammonds, J., Ahmed, M., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Data collection
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-11-20
  Changes: Structure summary