6H8B

Molybdenum storage protein prepared under in vivo-like conditions and incubated with ATP and molybdate at 303 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The molybdenum storage protein - A bionanolab for creating experimentally alterable polyoxomolybdate clusters.

Brunle, S.Poppe, J.Hail, R.Demmer, U.Ermler, U.

(2018) J Inorg Biochem 189: 172-179


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Molybdenum storage protein subunit betaA [auth B]269Azotobacter vinelandiiMutation(s): 0 
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84253 
Go to UniProtKB:  P84253
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Molybdenum storage protein subunit alphaB [auth A]275Azotobacter vinelandiiMutation(s): 0 
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84308 
Go to UniProtKB:  P84308
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J7T (Subject of Investigation/LOI)
Query on J7T

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C [auth B]molybdate cluster
Mo9 O31
OPVBNKHERKYGEI-UHFFFAOYSA-A
 Ligand Interaction
J8B (Subject of Investigation/LOI)
Query on J8B

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J [auth A]Molybdate cluster
Mo8 O26
VDJFCWAFEZEUOL-UHFFFAOYSA-A
 Ligand Interaction
J7Q (Subject of Investigation/LOI)
Query on J7Q

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G [auth A]tetrakis($l^{1}-oxidanyl)-[[2,2,2,4,4,4,4,6,6,6,8-undecakis($l^{1}-oxidanyl)-8-(oxidanylmolybdeniooxy)-6-[tris($l^{1}-oxidanyl)molybdeniooxy]-1,3,5,7-tetraoxa-2$l^{6},4$l^{6},6$l^{6},8$l^{4}-tetramolybdacyclooct-2-yl]oxy]molybdenum
H Mo7 O26
JETHCXFIMFVFFB-UHFFFAOYSA-A
 Ligand Interaction
FUQ (Subject of Investigation/LOI)
Query on FUQ

Download Ideal Coordinates CCD File 
F [auth B]Mo5 Cluster
H20 Mo5 O25
KKTGFJKWMBVMER-UHFFFAOYSA-A
 Ligand Interaction
J85 (Subject of Investigation/LOI)
Query on J85

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K [auth A][[[bis(oxidanylmolybdenio)-$l^{3}-oxidanyl]-$l^{1}-oxidanyl-oxidanylidene-molybdenio]-(oxidanylmolybdenio)-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)molybdenum
H3 Mo5 O11
VWFFRZIWORKLLY-UHFFFAOYSA-F
 Ligand Interaction
J8E (Subject of Investigation/LOI)
Query on J8E

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E [auth B]oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum
H2 Mo4 O10
DPQAEXIBFYBKAN-UHFFFAOYSA-G
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

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H [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
J7N (Subject of Investigation/LOI)
Query on J7N

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D [auth B]2,2,4-tris(oxidanyl)-1,3-dioxa-2$l^{4},4$l^{3}-dimolybdacyclobutane
H3 Mo2 O5
AUVZZTGQIKYYRK-UHFFFAOYSA-K
 Ligand Interaction
MOO (Subject of Investigation/LOI)
Query on MOO

Download Ideal Coordinates CCD File 
L [auth A]MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.72α = 90
b = 116.72β = 90
c = 235.42γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-08-02 
  • Released Date: 2019-02-20 
  • Deposition Author(s): Ermler, U., Poppe, J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection