2HVF | pdb_00002hvf

Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA

• PDB DOI: https://doi.org/10.2210/pdb2HVF/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Geobacillus stearothermophilus
• Mutation(s): Yes 


• Deposited: 2006-07-28 Released: 2007-06-12 
• Deposition Author(s): Anil, B., Kim, E.Y., Cho, J.H., Schindelin, H., Raleigh, D.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.208 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Detecting and quantifying strain in protein folding

Anil, B., Kim, E.Y., Cho, J.H., Schindelin, H., Raleigh, D.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.23 kDa 
• Atom Count: 494 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	A	52	N/A	Mutation(s): 1
UniProt
Find proteins for P02417 (Geobacillus stearothermophilus) Explore P02417  Go to UniProtKB:  P02417

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	J [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	K [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.208 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.517	α = 90
b = 53.517	β = 90
c = 36.178	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Anil, B., Kim, E.Y., Cho, J.H., Schindelin, H., Raleigh, D.P.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary