4NYP | pdb_00004nyp

The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii Cuta1 Complexed With NA+

• PDB DOI: https://doi.org/10.2210/pdb4NYP/pdb
• Entry: 4NYP supersedes: 4LU8

• Classification: METAL BINDING PROTEIN
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-11 Released: 2014-01-01 
• Deposition Author(s): Bagautdinov, B., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii Complexed with Na+

Bagautdinov, B., Tahirov, T.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.04 kDa 
• Atom Count: 5,895 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Divalent-cation tolerance protein CutA	A, B, C, D, E, F	102	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: cutA, PH0992
UniProt
Find proteins for O58720 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58720  Go to UniProtKB:  O58720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], O [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	G [auth A], H [auth A], N [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C, D, E, F	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.822	α = 90
b = 123.774	β = 90
c = 50.667	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-01 
Deposition Author(s): Bagautdinov, B., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 4LU8

Revision History  

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Other
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary