4WZZ

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTAS (Cphy_0583, TARGET EFI-511148) WITH BOUND L-RHAMNOSE

• PDB DOI: https://doi.org/10.2210/pdb4WZZ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Lachnoclostridium phytofermentans ISDg
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-20 Released: 2014-12-17 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.180 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTAS (Cphy_0583, TARGET EFI-511148) WITH BOUND L-RHAMNOSE

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 39.65 kDa 
• Atom Count: 2,712 
• Modelled Residue Count: 321 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar ABC transporter, substrate-binding protein	A	371	Lachnoclostridium phytofermentans ISDg	Mutation(s): 0  Gene Names: Cphy_0583
UniProt
Find proteins for A9KIX1 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)) Explore A9KIX1  Go to UniProtKB:  A9KIX1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAM	B [auth A]	alpha-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.70 Å
• R-Value Free: 0.180 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.625	α = 90
b = 87.625	β = 90
c = 83.982	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2017-03-15
  Changes: Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary