4H9D | pdb_00004h9d

Crystal Structure of Mn-dependent Gme HNH nicking endonuclease from Geobacter metallireducens GS-15, Northeast Structural Genomics Consortium (NESG) Target GmR87

• PDB DOI: https://doi.org/10.2210/pdb4H9D/pdb
• Entry: 4H9D supersedes: 2QGP

• Classification: HYDROLASE
• Organism(s): Geobacter metallireducens GS-15
• Mutation(s): No 


• Deposited: 2012-09-24 Released: 2012-10-10 
• Deposition Author(s): Kuzin, A., Chen, Y., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Owens, L., Chen, C.X., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.251 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target GmR87

Kuzin, A., Chen, Y., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Owens, L., Chen, C.X., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.37 kDa 
• Atom Count: 2,245 
• Modeled Residue Count: 268 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HNH endonuclease	A, B, C	112	Geobacter metallireducens GS-15	Mutation(s): 0
UniProt
Find proteins for Q39X46 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39X46  Go to UniProtKB:  Q39X46

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth B], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.251 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.674	α = 90
b = 83.385	β = 90
c = 225.116	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Kuzin, A., Chen, Y., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Owens, L., Chen, C.X., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)
• This entry supersedes: 2QGP

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary