3NET | pdb_00003net

Crystal structure of histidyl-tRNA synthetase from Nostoc sp. PCC 7120

• PDB DOI: https://doi.org/10.2210/pdb3NET/pdb

• Classification: LIGASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-09 Released: 2010-08-04 
• Deposition Author(s): Chang, C., Bigelow, L., Carroll, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of histidyl-tRNA synthetase from Nostoc sp. PCC 7120

Chang, C., Bigelow, L., Carroll, J., Joachimiak, 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)

Macromolecule Content 

• Total Structure Weight: 104.32 kDa 
• Atom Count: 6,572 
• Modeled Residue Count: 846 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidyl-tRNA synthetase	A, B	465	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: hisS, all5012 EC: 6.1.1.21
UniProt
Find proteins for Q8YMC2 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YMC2  Go to UniProtKB:  Q8YMC2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.656	α = 90
b = 73.656	β = 90
c = 521.912	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
CNS	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Chang, C., Bigelow, L., Carroll, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary