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(-) Description

Title :  STRUCTURE OF DELTA7-DGKA IN 7.9 MAG BY SERIAL FEMTOSECOND CRYSTATALLOGRAPHY TO 2.18 ANGSTROM RESOLUTION
 
Authors :  D. Li, N. Howe, O. Other, M. Caffrey
Date :  02 Sep 14  (Deposition) - 30 Sep 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Transferase, 7. 9 Mag, In Meso Crystallization, Lipid Cubic Phase, Lipidic Cubic Phase, Lipid Mesophase, Lipidic Mesophase, Membrane Protein, Microcrystals, Monoacylglycerol, Room Temperature Crystallography, Serial Femtosecond Crystallography, X-Ray Free-Electron Laser (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Li, P. J. Stansfeld, M. S. P. Sansom, A. Keogh, L. Vogeley, N. Howe, J. A. Lyons, D. Aragao, P. Fromme, R. Fromme, S. Basu, I. Grotjohann, C. Kupitz, K. Rendek, U. Weierstall, N. A. Zatsepin, V. Cherezov, W. Liu, S. Bandaru, N. J. English, C. Gati, A. Barty, O. Yefanov, H. N. Chapman, K. Diederichs, M. Messerschmidt, S. Boutet, G. J. Williams, M. Marvin Seibert, M. Caffrey
Ternary Structure Reveals Mechanism Of A Membrane Diacylglycerol Kinase.
Nat. Commun. V. 6 10140 2015
PubMed-ID: 26673816  |  Reference-DOI: 10.1038/NCOMMS10140

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE-DELTA 7
    Atcc: 29425
    Chains: A, B, C, D, E, F
    EC Number: 2.7.1.107
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHISB-DGKA-DELTA7
    Expression System Strain: WH1061
    Expression System Taxid: 562
    Expression System Vector: PTRCHISB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Synonym: DAGK, DIGLYCERIDE KINASE, DGK, DIACYLGLYCEROL KINASE-DELTA7

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
179M4Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
279N5Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
3FLC1Ligand/IonCITRATE ANION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
179M2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
279N3Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
3FLC-1Ligand/IonCITRATE ANION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
179M2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
279N2Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
3FLC1Ligand/IonCITRATE ANION
4ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:21 , ARG A:22 , TRP A:25BINDING SITE FOR RESIDUE 79N A1122
02AC2SOFTWAREALA B:46 , VAL B:50 , ALA B:52 , ARG B:55 , ILE C:114 , TRP C:117 , GLN D:33 , 79N D:1123BINDING SITE FOR RESIDUE 79M B1122
03AC3SOFTWAREGLU B:34 , CYS B:41 , VAL B:62 , GLU B:69 , TRP B:112BINDING SITE FOR RESIDUE 79N B1123
04AC4SOFTWAREASP B:49 , GLN D:33 , GLU D:34 , ILE D:105 , VAL D:109BINDING SITE FOR RESIDUE 79M B1124
05AC5SOFTWARELEU A:39 , LEU A:40 , GLU C:34 , GLU C:69 , TRP C:112BINDING SITE FOR RESIDUE 79N C1122
06AC6SOFTWAREGLN A:33 , 79M B:1122 , TRP C:117 , TRP D:25 , ALA D:29 , ARG D:32 , VAL D:36 , 79M D:1125BINDING SITE FOR RESIDUE 79N D1123
07AC7SOFTWAREILE B:26 , ARG B:32 , GLY B:35 , TRP D:47 , LEU D:48 , ASP D:49 , PHE D:120BINDING SITE FOR RESIDUE 79N D1124
08AC8SOFTWAREGLU A:34 , GLU A:69 , VAL A:101 , TRP D:25 , LEU D:39 , 79N D:1123BINDING SITE FOR RESIDUE 79M D1125
09AC9SOFTWAREGLU F:34 , GLU F:69 , ILE F:105 , ALA F:108 , VAL F:109 , TRP F:112 , LEU F:116BINDING SITE FOR RESIDUE 79M F1121
10BC1SOFTWAREGLU D:28 , GLU D:76 , FLC D:1126 , HOH D:2004BINDING SITE FOR RESIDUE ZN D1122
11BC2SOFTWAREGLU D:28 , GLU D:76 , ZN D:1122 , HOH D:2004 , HOH D:2028 , HOH D:2029 , HOH D:2030BINDING SITE FOR RESIDUE FLC D1126

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UYO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UYO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UYO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UYO)

(-) Exons   (0, 0)

(no "Exon" information available for 4UYO)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4uyo A   6 GFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    15        25        35        45        55        65        75        85        95       105       115      


Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4uyo B  24 AWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    33        43        53        63        73        83        93       103       113        


Chain C from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4uyo C  32 RQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    41        51        61        71        81        91       101       111       121


Chain D from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4uyo D  14 AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    23        33        43        53        63        73        83        93       103       113        


Chain E from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4uyo E  16 YSWKGLRAAWIRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    25||      40        50        60        70        80        90       100       110       120 
                                     26|                                                                                         
                                      32                                                                                         


Chain F from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4uyo F  26 INEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    35        45        55        65        75        85        95       105       115
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4UYO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UYO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UYO)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KDGL_ECOLI | P0ABN1: 2kdc 3ze3 3ze4 3ze5 4bpd 4brb 4brr 4cjz 4ck0 4d2e 4up6 4uxw 4uxx 4uxz 5d56 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

4uxw STRUCTURE OF DELTA4-DGKA-APO IN 9.9 MAG
4uxx STRUCTURE OF DELTA4-DGKA WITH AMPPCP IN 9.9 MAG
4uxz STRUCTURE OF DELTA7-DGKA-SYN IN 7.9 MAG TO 2.18 ANGSTROM RESOLUTION