6JBO | pdb_00006jbo

Crystal structure of EfeO-like protein Algp7 containing samarium ion

• PDB DOI: https://doi.org/10.2210/pdb6JBO/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Sphingomonas sp. A1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-26 Released: 2020-01-29 
• Deposition Author(s): Okumura, K., Takase, R., Maruyama, Y., Mikami, B., Murata, K., Hashimoto, W.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Rare metal binding by a cell-surface component of bacterial EfeUOB iron importer

Okumura, K., Takase, R., Maruyama, Y., Mikami, B., Murata, K., Hashimoto, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.86 kDa 
• Atom Count: 4,455 
• Modeled Residue Count: 502 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate-binding protein	A, B	251	Sphingomonas sp. A1	Mutation(s): 0  Gene Names: p7
UniProt
Find proteins for Q25C86 (Sphingomonas sp. A1) Explore Q25C86  Go to UniProtKB:  Q25C86

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	I [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.833	α = 90
b = 97.509	β = 90
c = 104.906	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
MOLREP	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Okumura, K., Takase, R., Maruyama, Y., Mikami, B., Murata, K., Hashimoto, W.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 2.0: 2023-10-18
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-22
  Changes: Refinement description