6GY3 | pdb_00006gy3

Crystal Structure of C. glutamicum AmtR bound to glnA operator DNA

• PDB DOI: https://doi.org/10.2210/pdb6GY3/pdb
• NAKB: 6GY3

• Classification: TRANSCRIPTION
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-28 Released: 2019-07-10 
• Deposition Author(s): Sevvana, M., Muller, Y.A.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

The role of DNA flexibility in transcription regulator AmtR-DNA interaction

Schwab, C., Sevvana, M., Seidel, G., Sandmann, A., Grau, F.C., Muller, Y.A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.68 kDa 
• Atom Count: 3,872 
• Modeled Residue Count: 440 
• Deposited Residue Count: 440 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmtR protein	A, B	202	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: amtR
UniProt
Find proteins for Q79VH8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q79VH8  Go to UniProtKB:  Q79VH8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*TP*AP*TP*AP*GP*AP*TP*CP*GP*AP*TP*AP*GP*AP*C)-3')	C	18	Corynebacterium glutamicum

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*TP*AP*TP*CP*GP*AP*TP*CP*TP*AP*TP*AP*GP*AP*C)-3')	D	18	Corynebacterium glutamicum

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.32	α = 90
b = 76.15	β = 90
c = 117.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Sevvana, M., Muller, Y.A.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SPP1395

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2020-03-18
  Changes: Derived calculations
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description