5FHV

Crystal structure of mCherry after reaction with 2-mercaptoethanol

> Summary

Summary for 5FHV

Related2H5Q
DescriptormCherry-BME, TRIETHYLENE GLYCOL, BETA-MERCAPTOETHANOL, ... (5 entities in total)
Functional Keywordsfluorescent protein, 2-mercaptoethanol, michael addition
Biological sourceDiscosoma sp.
Total number of polymer chains1
Total molecular weight31156.14
Authors
De Zitter, E.,Dedecker, P.,Van Meervelt, L. (deposition date: 2015-12-22, release date: 2017-01-11)
Primary citation
Cloin, B.M.C.,De Zitter, E.,Gielen, V.,Mikhaylova, M.,Hoogenraad, C.C.,Dedecker, P.,Kapitein, L.C.
RFP caging by reversible Michael addition of BME enables localization microscopy RFP-based localization microscopy through reversible Michael addition of BME
To Be Published,
Experimental method
X-RAY DIFFRACTION (1.55 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.188500.5%2.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5fhv
no rotation
Molmil generated image of 5fhv
rotated about x axis by 90°
Molmil generated image of 5fhv
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AmCherry-BMEpolymer26930489.21
Pfam (PF01353)
UniProt (by SIFTS) (D0VWW2)
Discosoma sp.
TRIETHYLENE GLYCOLnon-polymer150.21
BETA-MERCAPTOETHANOLnon-polymer78.13
HEXAETHYLENE GLYCOLnon-polymer282.31
waterwater18.0315

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight30489.2
Non-Polymers*Number of molecules5
Total molecular weight666.9
All*Total molecular weight31156.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.55 Å)

Cell axes48.78343.24461.234
Cell angles90.00111.5290.00
SpacegroupP 1 21 1
Resolution limits45.38 - 1.55
the highest resolution shell value1.596 - 1.550
R-factor0.1583
R-work0.15670
the highest resolution shell value0.234
R-free0.18760
the highest resolution shell value0.276
RMSD bond length0.006
RMSD bond angle1.325

Data Collection Statistics

Resolution limits45.38 - 1.55
the highest resolution shell value -
Number of reflections34495
Rmerge_l_obs0.062
the highest resolution shell value0.562
Completeness99.4
Redundancy3.3
the highest resolution shell value3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.4289

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0008218biological_processbioluminescence
A0006091biological_processgeneration of precursor metabolites and energy
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15binding site for residue PGE A 301
ChainResidue
AALA145
ASER146
AASN196
ALYS198
AARG216

AC26binding site for residue BME A 302
ChainResidue
AASN98
APHE99
AGLU100
AASP174
AGLU176
AHOH598

AC31binding site for residue BME A 303
ChainResidue
ALYS121

AC43binding site for residue BME A 304
ChainResidue
ALYS92
AGLU94
ATHR180

AC54binding site for residue P6G A 305
ChainResidue
ALYS15
AGLN114
AGLU117
AILE119

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
MCQ_5fhv_A_6629{(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid binding site
ChainResidueligand
APHE14MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN42-ALA44MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER62-PHE65MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER69-LYS70MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AVAL73MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATRP93MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AARG95MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN109MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER111MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATYR120MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATRP143-GLU144MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER146MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLU148MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AILE161MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN163MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATYR181MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AVAL195MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AILE197MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ALEU199MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN213MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLU215MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AALA217MCQ: {(4S)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-4-[(S)-[(2-hydroxyethyl)sulfanyl](4-hydroxyphenyl)methyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid

BME_5fhv_A_3036BETA-MERCAPTOETHANOL binding site
ChainResidueligand
ALYS15-HIS17BME: BETA-MERCAPTOETHANOL
AILE119-LYS121BME: BETA-MERCAPTOETHANOL

P6G_5fhv_A_3055HEXAETHYLENE GLYCOL binding site
ChainResidueligand
ALYS15P6G: HEXAETHYLENE GLYCOL
AGLN114-ASP115P6G: HEXAETHYLENE GLYCOL
AGLU117P6G: HEXAETHYLENE GLYCOL
AILE119P6G: HEXAETHYLENE GLYCOL

CH6_5fhv_A_6624{(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid binding site
ChainResidueligand
AGLN42-ALA44CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER62-PHE65CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER69-LYS70CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATRP93CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AARG95CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN109CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATYR120CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATRP143-GLU144CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ASER146CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AILE161CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN163CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ATYR181CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AILE197CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
ALEU199CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
AGLN213-GLU215CH6: {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid

BME_5fhv_A_3046BETA-MERCAPTOETHANOL binding site
ChainResidueligand
ALYS92-GLU94BME: BETA-MERCAPTOETHANOL
ATHR180-LYS182BME: BETA-MERCAPTOETHANOL

BME_5fhv_A_3027BETA-MERCAPTOETHANOL binding site
ChainResidueligand
AASN98-GLU100BME: BETA-MERCAPTOETHANOL
ALYS162BME: BETA-MERCAPTOETHANOL
AASP174-GLU176BME: BETA-MERCAPTOETHANOL

PGE_5fhv_A_3019TRIETHYLENE GLYCOL binding site
ChainResidueligand
AALA145-SER147PGE: TRIETHYLENE GLYCOL
AASN196-LYS198PGE: TRIETHYLENE GLYCOL
AARG216-GLU218PGE: TRIETHYLENE GLYCOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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