5O5W | pdb_00005o5w

Molybdenum storage protein room-temperature structure determined by serial millisecond crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.201 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.198 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons.

Weinert, T.Olieric, N.Cheng, R.Brunle, S.James, D.Ozerov, D.Gashi, D.Vera, L.Marsh, M.Jaeger, K.Dworkowski, F.Panepucci, E.Basu, S.Skopintsev, P.Dore, A.S.Geng, T.Cooke, R.M.Liang, M.Prota, A.E.Panneels, V.Nogly, P.Ermler, U.Schertler, G.Hennig, M.Steinmetz, M.O.Wang, M.Standfuss, J.

(2017) Nat Commun 8: 542-542

  • DOI: https://doi.org/10.1038/s41467-017-00630-4
  • Primary Citation Related Structures: 
    5NJM, 5NLX, 5NM2, 5NM4, 5NM5, 5NQT, 5NQU, 5O5W

  • PubMed Abstract: 

    Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000-10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons.Serial crystallography was developed for protein crystal data collection with X-ray free-electron lasers. Here the authors present several examples which show that serial crystallography using high-viscosity injectors can also be routinely employed for room-temperature data collection at synchrotrons.


  • Organizational Affiliation
    • Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 63.32 kDa 
  • Atom Count: 4,111 
  • Modeled Residue Count: 511 
  • Deposited Residue Count: 546 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit alpha276Azotobacter vinelandii DJMutation(s): 0 
Gene Names: mosAAvin_43200
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84308 
Go to UniProtKB:  P84308
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84308
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit beta270Azotobacter vinelandii DJMutation(s): 0 
Gene Names: mosBAvin_43210
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84253 
Go to UniProtKB:  P84253
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84253
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8M0

Query on 8M0



Download:Ideal Coordinates CCD File
E [auth A],
O [auth B]
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
ATP

Query on ATP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
M10

Query on M10



Download:Ideal Coordinates CCD File
F [auth A](mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI)
Mo3 O13
HGNGIYFURFJYFJ-UHFFFAOYSA-N
MO

Query on MO



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
G [auth A]
H [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.201 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.198 (DCC) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.35α = 90
b = 117.35β = 90
c = 233.35γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description