5YCF | pdb_00005ycf

Crystal structure of Xiphophorus maculatus adenylate kinase

• PDB DOI: https://doi.org/10.2210/pdb5YCF/pdb

• Classification: TRANSFERASE
• Organism(s): Xiphophorus maculatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-07 Released: 2018-09-12 
• Deposition Author(s): Bae, E., Kim, J., Moon, S.
• Funding Organization(s): Rural Development Administration, National Research Foundation of Korea

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Xiphophorus maculatus adenylate kinase

Bae, E., Kim, J., Moon, S.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 44.22 kDa 
• Atom Count: 3,351 
• Modeled Residue Count: 377 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase isoenzyme 1	A [auth B], B [auth A]	193	Xiphophorus maculatus	Mutation(s): 0  Gene Names: AK1 EC: 2.7.4.3 (PDB Primary Data), 2.7.4.6 (PDB Primary Data)
UniProt
Find proteins for M4AA20 (Xiphophorus maculatus) Explore M4AA20  Go to UniProtKB:  M4AA20

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5	C [auth B], D [auth A]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.033	α = 90
b = 79.779	β = 90
c = 122.386	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Bae, E., Kim, J., Moon, S.

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Funding Organization	Location	Grant Number
Rural Development Administration	Korea, Republic Of	PJ01111201
National Research Foundation of Korea	Korea, Republic Of	NRF-2016R1D1A1A09916821

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description