7EPK | pdb_00007epk

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 (Depositor), 0.262 (DCC)
R-Value Work:
0.224 (Depositor), 0.225 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YB62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.258 (Depositor), 0.262 (DCC)
R-Value Work: 0.224 (Depositor), 0.225 (DCC)
R-Value Observed: 0.226 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.