4KAL | pdb_00004kal

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with quinoline-3-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb4KAL/pdb

• Classification: TRANSFERASE
• Organism(s): Rhizobium etli CFN 42
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-22 Released: 2013-05-22 
• Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.190 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with quinoline-3-carboxylic acid

Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C.

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: 78.97 kDa 
• Atom Count: 5,715 
• Modeled Residue Count: 660 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable sugar kinase protein	A, B	352	Rhizobium etli CFN 42	Mutation(s): 0  Gene Names: RHE_CH00135
UniProt
Find proteins for Q2KDX6 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2KDX6  Go to UniProtKB:  Q2KDX6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	C [auth A], H [auth B]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
Q3C	D [auth A], I [auth B]	quinoline-3-carboxylic acid C10 H7 N O2 DJXNJVFEFSWHLY-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], J [auth B], K [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
K	G [auth A], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-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:  0.190 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.181	α = 90
b = 81.219	β = 98.17
c = 82.95	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary