4K93

CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE

• PDB DOI: https://doi.org/10.2210/pdb4K93/pdb

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


• Deposited: 2013-04-19 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: 0.222 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE

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.

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.

Macromolecule Content

• Total Structure Weight: 79.83 kDa 
• Atom Count: 5,842 
• Modelled Residue Count: 660 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sugar kinase	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], L [auth B]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
1Q8	D [auth A], G [auth A], H [auth A], I [auth A], K [auth B], M [auth B], P [auth B], Q [auth B]	N-(hydroxymethyl)benzamide C8 H9 N O2 UOUBPDZUBVJZOQ-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], N [auth B], O [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
K	J [auth A], R [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: 0.222 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.438	α = 90
b = 91.184	β = 90
c = 92.292	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: 2024-10-30
  Changes: Structure summary