8HIG | pdb_00008hig

Co-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA

• PDB DOI: https://doi.org/10.2210/pdb8HIG/pdb
• NAKB: 8HIG

• Classification: TRANSCRIPTION/DNA
• Organism(s): Saccharopolyspora erythraea NRRL 2338
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-20 Released: 2023-11-22 
• Deposition Author(s): Lin, W., Xu, J.C., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.325 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.265 (Depositor) 

Starting Model: experimental

Literature

Co-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA

Lin, W., Xu, J.C., Zhang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
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: 67.52 kDa 
• Atom Count: 2,353 
• Modeled Residue Count: 228 
• Deposited Residue Count: 552 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response OmpR family regulator	A, B	256	Saccharopolyspora erythraea NRRL 2338	Mutation(s): 0  Gene Names: glnR
UniProt
Find proteins for A4FQD5 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)) Explore A4FQD5  Go to UniProtKB:  A4FQD5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')	C [auth D]	20	Saccharopolyspora erythraea NRRL 2338

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')	D [auth C]	20	Saccharopolyspora erythraea NRRL 2338

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.325 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.265 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.279	α = 90
b = 46.279	β = 90
c = 366.859	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Lin, W., Xu, J.C., Zhang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81903526

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release