7EPK

Crystal Structure of Signal Recognition Particle 54 kDa protein (SRP54) from Aeropyrum pernix K1 in Complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb7EPK/pdb

• Classification: HYDROLASE
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-27 Released: 2021-05-19 
• Deposition Author(s): Xie, Y., Zhang, B., Liu, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Starting Model: experimental

Literature

Crystal Structure of Signal Recognition Particle 54 kDa protein (SRP54) from Aeropyrum pernix K1 in Complex with GDP

Xie, Y., Zhang, B., Liu, J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 49.66 kDa 
• Atom Count: 3,383 
• Modelled Residue Count: 426 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle 54 kDa protein	A	441	Aeropyrum pernix K1	Mutation(s): 0  Gene Names: srp54, APE_1735 EC: 3.6.5.4
UniProt
Find proteins for Q9YB62 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YB62  Go to UniProtKB:  Q9YB62

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.498	α = 90
b = 82.498	β = 90
c = 140.805	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Xie, Y., Zhang, B., Liu, J.

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description