4ZHN | pdb_00004zhn

Crystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T

• PDB DOI: https://doi.org/10.2210/pdb4ZHN/pdb
• NAKB: 4ZHN

• Classification: Oxidoreductase/DNA
• Organism(s): synthetic construct, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-25 Released: 2015-12-23 
• Deposition Author(s): Ergel, B., Yu, B., Vorobiev, S.M., Forouhar, F., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
• 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: 1.33 Å
• R-Value Free: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

Starting Model: experimental

Literature

DFT Studies of the Rate-Limiting Step in the Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related Experimental Studies

Hall, M.L., Ergel, B., Miller, E.B., Yu, B., Rinaldo, D., Hunt, J.F., Friesner, R.

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: 24.68 kDa 
• Atom Count: 1,963 
• Modeled Residue Count: 204 
• Deposited Residue Count: 214 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase AlkB	B [auth A]	211	Escherichia coli K-12	Mutation(s): 1  Gene Names: alkB, aidD, b2212, JW2200 EC: 1.14.11.33
UniProt
Find proteins for P05050 (Escherichia coli (strain K12)) Explore P05050  Go to UniProtKB:  P05050

Entity ID: 1
Molecule	Chains	Length	Organism	Image
methylated trinucleotide DNA T-meA-T	A [auth B]	3	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.373	α = 90
b = 41.373	β = 90
c = 116.569	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction
COMO	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Ergel, B., Yu, B., Vorobiev, S.M., Forouhar, F., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM077360

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2017-11-29
  Changes: Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description