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PDBsum entry 5d9c
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PDB id:
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Hydrolase
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Title:
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Luciferin-regenerating enzyme solved by siras using xfel (refined against hg derivative data)
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Structure:
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Luciferin regenerating enzyme. Chain: a. Engineered: yes
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Source:
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Photinus pyralis. Common eastern firefly. Organism_taxid: 7054. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Resolution:
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1.60Å
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R-factor:
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0.203
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R-free:
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0.235
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Authors:
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K.Yamashita,D.Pan,T.Okuda,T.Murai,A.Kodan,T.Yamaguchi,K.Gomi, N.Kajiyama,H.Kato,H.Ago,M.Yamamoto,T.Nakatsu
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Key ref:
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K.Yamashita
et al.
(2015).
An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep,
5,
14017.
PubMed id:
DOI:
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Date:
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18-Aug-15
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Release date:
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23-Sep-15
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PROCHECK
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Headers
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References
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Q95YI4
(Q95YI4_PHOPY) -
Luciferin regenerating enzyme from Photinus pyralis
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Seq:
Struc:
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308 a.a.
307 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 3 residue positions (black
crosses)
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DOI no:
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Sci Rep
5:14017
(2015)
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PubMed id:
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An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
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K.Yamashita,
D.Pan,
T.Okuda,
M.Sugahara,
A.Kodan,
T.Yamaguchi,
T.Murai,
K.Gomi,
N.Kajiyama,
E.Mizohata,
M.Suzuki,
E.Nango,
K.Tono,
Y.Joti,
T.Kameshima,
J.Park,
C.Song,
T.Hatsui,
M.Yabashi,
S.Iwata,
H.Kato,
H.Ago,
M.Yamamoto,
T.Nakatsu.
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ABSTRACT
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Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs)
holds great potential for structure determination of challenging proteins that
are not amenable to producing large well diffracting crystals. Efficient de novo
phasing methods are highly demanding and as such most SFX structures have been
determined by molecular replacement methods. Here we employed single isomorphous
replacement with anomalous scattering (SIRAS) for phasing and demonstrate
successful application to SFX de novo phasing. Only about 20,000 patterns in
total were needed for SIRAS phasing while single wavelength anomalous dispersion
(SAD) phasing was unsuccessful with more than 80,000 patterns of derivative
crystals. We employed high energy X-rays from SACLA (12.6 keV) to take
advantage of the large anomalous enhancement near the LIII absorption edge of
Hg, which is one of the most widely used heavy atoms for phasing in conventional
protein crystallography. Hard XFEL is of benefit for de novo phasing in the use
of routinely used heavy atoms and high resolution data collection.
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