3G9C

Crystal structure of the product Bacillus anthracis glmS ribozyme

• PDB DOI: https://doi.org/10.2210/pdb3G9C/pdb
• NAKB: 3G9C

• Classification: RNA binding protein/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-13 Released: 2009-11-03 
• Deposition Author(s): Strobel, S.A., Cochrane, J.C., Lipchock, S.V., Smith, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.307 
• R-Value Work: 0.246 
• R-Value Observed: 0.249 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 242.21 kDa 
• Atom Count: 15,856 
• Modelled Residue Count: 966 
• Deposited Residue Count: 1,000 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	A, D [auth B], G [auth C], J [auth D]	98	Homo sapiens	Mutation(s): 2  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012 GTEx:  ENSG00000077312

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')	B [auth E], E [auth F], H [auth G], K [auth H]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
GLMS RIBOZYME	C [auth P], F [auth Q], I [auth R], L [auth S]	141	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLP	M [auth E]	2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C6 H14 N O8 P XHMJOUIAFHJHBW-UKFBFLRUSA-N
MG	N [auth P], O [auth Q], P [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.307 
• R-Value Work: 0.246 
• R-Value Observed: 0.249 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.586	α = 90
b = 229.827	β = 90.16
c = 101.75	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Strobel, S.A., Cochrane, J.C., Lipchock, S.V., Smith, K.D.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection, Database references
• Version 1.4: 2018-04-11
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2021-10-20
  Changes: Database references, Structure summary
• Version 1.7: 2024-02-21
  Changes: Data collection