3OEE

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of four mutant forms of yeast F1 ATPase: alpha-F405S

Arsenieva, D.Symersky, J.Wang, Y.Pagadala, V.Mueller, D.M.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C, J, K
A, B, C, J, K, L, S, T, U
510Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: ATP1YBL099WYBL0827
EC: 3.6.3.14
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP07251
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F, M, N
D, E, F, M, N, O, V, W, X
484Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP2YJR121WJ2041
EC: 3.6.3.14
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00830
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gamma
G, P, Y
278Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP3ATP3aATP3bYBR039WYBR0408
EC: 3.6.3.14
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta
H, Q, Z
138Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP16YDL004WYD8119.03D2935
EC: 3.6.3.14
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilonAA [auth 1],
I,
R
61Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP15YPL271WP0345
EC: 3.6.3.14
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
BA [auth A]
BB [auth U]
DA [auth B]
DB [auth V]
FA [auth C]
BA [auth A],
BB [auth U],
DA [auth B],
DB [auth V],
FA [auth C],
FB [auth X],
HA [auth D],
KA [auth F],
MA [auth J],
OA [auth K],
QA [auth L],
SA [auth M],
VA [auth O],
XA [auth S],
ZA [auth T]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
JA [auth E],
UA [auth N]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth T]
CA [auth A]
CB [auth U]
EA [auth B]
EB [auth V]
AB [auth T],
CA [auth A],
CB [auth U],
EA [auth B],
EB [auth V],
GA [auth C],
GB [auth X],
IA [auth D],
LA [auth F],
NA [auth J],
PA [auth K],
RA [auth L],
TA [auth M],
WA [auth O],
YA [auth S]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.43α = 90
b = 288.58β = 101.37
c = 187.17γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description