5L7P

In silico-powered specific incorporation of photocaged Dopa at multiple protein sites

> Summary

Summary for 5L7P

DescriptorTyrosine--tRNA ligase, PENTAETHYLENE GLYCOL, CALCIUM ION, ... (6 entities in total)
Functional Keywordstyrrs, ligase
Biological sourceMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Cellular locationCytoplasm Q57834
Total number of polymer chains2
Total molecular weight73378.63
Authors
Primary citation
Hauf, M.,Richter, F.,Schneider, T.,Faidt, T.,Martins, B.M.,Baumann, T.,Durkin, P.,Dobbek, H.,Jacobs, K.,Moglich, A.,Budisa, N.
Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code.
Chembiochem, 2017
PubMed: 28650092 (PDB entries with the same primary citation)
DOI: 10.1002/cbic.201700327
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.9 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.217401.0%2.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5l7p
no rotation
Molmil generated image of 5l7p
rotated about x axis by 90°
Molmil generated image of 5l7p
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5l7p
no rotation
Molmil generated image of 5l7p
rotated about x axis by 90°
Molmil generated image of 5l7p
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5l7p.pdb1.gz [202.88 KB])
Coordinate files for Biological unit (5l7p.pdb2.gz [202.1 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BTyrosine--tRNA ligasepolymer31836366.32
UniProt (Q57834)
Pfam (PF00579)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Tyrosyl-tRNA synthetase,TyrRS
PENTAETHYLENE GLYCOLnon-polymer238.31
CALCIUM IONnon-polymer40.11
CHLORIDE IONnon-polymer35.51
(2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acidnon-polymer332.31
waterwater18.0341

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight72732.5
Non-Polymers*Number of molecules4
Total molecular weight646.1
All*Total molecular weight73378.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.9 Å)

Cell axes55.50778.275137.883
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits43.24 - 1.90
the highest resolution shell value1.956 - 1.900
R-factor0.1797
R-work0.17830
the highest resolution shell value0.240
R-free0.21760
the highest resolution shell value0.308
RMSD bond length0.012
RMSD bond angle1.189

Data Collection Statistics

Resolution limits43.24 - 1.90
the highest resolution shell value -
Number of reflections48252
Completeness99.7
Redundancy10.2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5293

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
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17binding site for residue 1PE A 401
ChainResidue
ALEU69
ALEU73
AASN74
AALA147
AMET154
AGLN155
ACL403

AC25binding site for residue CA A 402
ChainResidue
AGLU221
AHOH541
AHOH570
AHOH653
BHOH603

AC36binding site for residue CL A 403
ChainResidue
AALA67
AASP68
ALEU69
AALA70
AGLY105
A1PE401

AC413binding site for residue BUU B 401
ChainResidue
BGLY34
BGLU36
BILE65
BALA67
BLEU69
BALA70
BGLY105
BALA109
BTYR151
BMET154
BGLN155
BALA158
BGLN173

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

site_idNumber of ResiduesDetails
1PE_5l7p_A_40118PENTAETHYLENE GLYCOL binding site
ChainResidueligand
AILE651PE: PENTAETHYLENE GLYCOL
AALA671PE: PENTAETHYLENE GLYCOL
ALEU69-ALA701PE: PENTAETHYLENE GLYCOL
ALEU73-ASN741PE: PENTAETHYLENE GLYCOL
AGLY1051PE: PENTAETHYLENE GLYCOL
APHE108-LEU1101PE: PENTAETHYLENE GLYCOL
ATYR1141PE: PENTAETHYLENE GLYCOL
AALA147-GLU1481PE: PENTAETHYLENE GLYCOL
AILE150-TYR1511PE: PENTAETHYLENE GLYCOL
AMET154-GLN1551PE: PENTAETHYLENE GLYCOL
AALA1581PE: PENTAETHYLENE GLYCOL

BUU_5l7p_B_40130(2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid binding site
ChainResidueligand
BALA32-GLU36BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BILE65-ALA70BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BLEU73BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BGLY105-SER106BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BPHE108-ALA109BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BTYR114BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BILE137BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BILE150-PRO152BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BMET154-GLN155BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BALA158BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BMET162BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BASN167BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BGLU172-GLN173BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid
BILE176-HIS177BUU: (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid

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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
SWS_FT_FI11ATP. {ECO:0000255}.
ChainResidueDetails
ASER219

SWS_FT_FI23Tyrosine. {ECO:0000269|PubMed:12754495}.
ChainResidueDetails
AALA44
AGLU48
AGLN185

SWS_FT_FI31Interaction with t-RNA.
ChainResidueDetails
AASN155

SWS_FT_FI41ATP. {ECO:0000255}.
ChainResidueDetails
BSER219

SWS_FT_FI53Tyrosine. {ECO:0000269|PubMed:12754495}.
ChainResidueDetails
BALA44
BGLU48
BGLN185

SWS_FT_FI61Interaction with t-RNA.
ChainResidueDetails
BASN155

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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