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(-) Description

Title :  DARK-STATE STRUCTURE OF SFGFP CONTAINING THE UNNATURAL AMINO ACID P-AZIDO-PHENYLALANINE AT RESIDUE 66
 
Authors :  S. C. Reddington, D. D. Jones, P. J. Rizkallah, E. M. Tippmann
Date :  14 Feb 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Barrel, Fluorescent Protein, Chromophore By Cyclisation, P- Azido-L-Phenylalanine, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Reddington, P. J. Rizkallah, P. D. Watson, R. Pearson, E. M. Tippmann, D. D. Jones
Different Photochemical Events Of A Genetically Encoded Phenyl Azide Define And Modulate Gfp Fluorescence.
Angew. Chem. Int. Ed. Engl. V. 52 5974 2013
PubMed-ID: 23620472  |  Reference-DOI: 10.1002/ANIE.201301490

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: DH10B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GFP
    Mutation: YES
    Organism Common: JELLYFISH
    Organism Scientific: AEQUOREA VICTORIA
    Organism Taxid: 6100

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 38)

Asymmetric Unit (4, 38)
No.NameCountTypeFull Name
1CQ12Mod. Amino Acid[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-AZIDOBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2EDO24Ligand/Ion1,2-ETHANEDIOL
3SO49Ligand/IonSULFATE ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (4, 27)
No.NameCountTypeFull Name
1CQ11Mod. Amino Acid[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-AZIDOBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2EDO19Ligand/Ion1,2-ETHANEDIOL
3SO44Ligand/IonSULFATE ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1CQ11Mod. Amino Acid[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-AZIDOBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2EDO5Ligand/Ion1,2-ETHANEDIOL
3SO45Ligand/IonSULFATE ION
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:55 , PRO A:56 , TRP A:57 , PRO A:58 , HIS A:139 , HOH A:411 , HOH A:415 , HOH A:424 , HOH A:438 , HOH A:497 , HOH A:552BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREHIS A:148 , ASN A:149 , TYR A:151 , ARG A:168 , ARG B:73BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREASN A:164 , PHE A:165 , LYS A:166 , ASP A:180 , HIS A:181 , HOH A:457BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREASP A:19 , GLY A:20 , ASP A:21 , GLU A:124 , LEU A:125 , LYS A:126BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLU A:6 , THR A:9 , ARG A:30 , GLU A:32 , LYS A:45 , ILE A:47 , HOH A:559BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREPRO A:13 , ILE A:14 , LEU A:15 , GLU A:32 , GLY A:33BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREVAL A:11 , ARG A:80 , HOH A:560BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREGLU A:34 , THR A:43 , HOH A:483 , HOH A:576 , SO4 B:301BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREPRO A:89 , EDO A:313 , HOH A:421 , HOH A:510 , HOH A:567 , HOH A:587 , PRO B:211 , HOH B:450BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWAREASN A:144 , EDO A:311 , HOH A:482BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREGLU A:142 , TYR A:143 , ASN A:144 , EDO A:310BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWAREPRO A:89 , GLU A:90 , LYS A:113 , PHE A:114 , HOH A:484 , LYS B:209 , PRO B:211 , HOH B:450BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWARELYS A:3 , LEU A:7 , EDO A:309 , HOH A:510 , HOH A:528 , HOH A:571BINDING SITE FOR RESIDUE EDO A 313
14BC5SOFTWARESER A:208 , LYS A:209 , PRO A:211 , HOH A:522BINDING SITE FOR RESIDUE EDO A 314
15BC6SOFTWAREHOH A:573BINDING SITE FOR RESIDUE EDO A 315
16BC7SOFTWAREGLU A:17 , ASP A:19 , ILE A:123BINDING SITE FOR RESIDUE EDO A 316
17BC8SOFTWAREARG A:109 , ARG A:122 , GLU A:124BINDING SITE FOR RESIDUE EDO A 317
18BC9SOFTWAREHIS A:25 , LYS A:26 , HOH A:488BINDING SITE FOR RESIDUE EDO A 318
19CC1SOFTWARELYS A:107 , ARG A:109 , GLU A:124 , HOH A:549 , HOH A:580 , LEU B:194BINDING SITE FOR RESIDUE EDO A 319
20CC2SOFTWAREALA A:154 , LEU A:195 , ASP A:197BINDING SITE FOR RESIDUE EDO A 320
21CC3SOFTWAREHOH A:550 , LYS B:209 , GLU B:213 , ARG B:215 , ASP B:216 , HIS B:217BINDING SITE FOR RESIDUE EDO A 321
22CC4SOFTWAREALA A:163 , TYR A:182 , GLN A:183 , GLN A:184 , GLY B:191BINDING SITE FOR RESIDUE EDO A 322
23CC5SOFTWAREGLU A:132BINDING SITE FOR RESIDUE EDO A 323
24CC6SOFTWAREARG A:73 , PRO A:75 , ASP A:76 , HIS A:77 , ASN B:149 , TYR B:151BINDING SITE FOR RESIDUE TRS A 324
25CC7SOFTWAREARG A:80 , GLU A:115 , GLY A:116 , ASP A:117 , THR A:118 , HOH A:562 , HOH A:584 , HOH B:485BINDING SITE FOR RESIDUE TRS A 325
26CC8SOFTWARESER A:99 , PHE A:100 , LYS A:101 , ASP A:102 , ASP A:103 , HOH A:417BINDING SITE FOR RESIDUE TRS A 326
27CC9SOFTWARELYS A:41 , EDO A:308 , ASN B:144 , PHE B:145 , VAL B:206 , LEU B:207 , HOH B:502BINDING SITE FOR RESIDUE SO4 B 301
28DC1SOFTWAREPHE B:100 , LYS B:101 , ASP B:102 , ASP B:103 , HOH B:444BINDING SITE FOR RESIDUE SO4 B 302
29DC2SOFTWARELYS B:107 , THR B:108 , ARG B:109 , GLU B:124 , LYS B:126BINDING SITE FOR RESIDUE SO4 B 303
30DC3SOFTWAREHIS B:148 , ASN B:149 , PHE B:165 , LYS B:166BINDING SITE FOR RESIDUE SO4 B 304
31DC4SOFTWAREGLU B:95 , ARG B:96 , THR B:97 , TYR B:182 , GLN B:183 , GLN B:184 , HOH B:524BINDING SITE FOR RESIDUE SO4 B 305
32DC5SOFTWAREARG B:30 , GLU B:32 , LYS B:45 , ILE B:47 , HOH B:402BINDING SITE FOR RESIDUE EDO B 306
33DC6SOFTWAREGLU B:17 , ILE B:123 , EDO B:308BINDING SITE FOR RESIDUE EDO B 307
34DC7SOFTWAREARG B:109 , ARG B:122 , GLU B:124 , EDO B:307BINDING SITE FOR RESIDUE EDO B 308
35DC8SOFTWARETYR A:151 , ASP B:76BINDING SITE FOR RESIDUE EDO B 309
36DC9SOFTWAREHIS B:25BINDING SITE FOR RESIDUE EDO B 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J88)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:88 -Pro A:89
2Met B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J88)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J88)

(-) Exons   (0, 0)

(no "Exon" information available for 4J88)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains d4j88a_ A: Green fluorescent protein, GFP                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j88 A   2 SKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLtVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITH 231
                                    11        21        31        41        51        61  |||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         64||                                                                                                                                                                   
                                                                                          66-CQ1                                                                                                                                                                
                                                                                           68                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains d4j88b_ B: Green fluorescent protein, GFP                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j88 B   3 KGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLtVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITH 231
                                    12        22        32        42        52        62 |||    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
                                                                                        64||                                                                                                                                                                   
                                                                                         66-CQ1                                                                                                                                                                
                                                                                          68
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J88)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J88)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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        GFP_AEQVI | P42212: 1b9c 1bfp 1c4f 1cv7 1ema 1emb 1emc 1eme 1emf 1emg 1emk 1eml 1emm 1f09 1f0b 1gfl 1h6r 1hcj 1huy 1jby 1jbz 1jc0 1jc1 1kp5 1kyp 1kyr 1kys 1myw 1q4a 1q4b 1q4c 1q4d 1q4e 1q73 1qxt 1qy3 1qyf 1qyo 1qyq 1rm9 1rmm 1rmo 1rmp 1rrx 1s6z 1w7s 1w7t 1w7u 1yfp 1yhg 1yhh 1yhi 1yj2 1yjf 1z1p 1z1q 2ah8 2aha 2awj 2awk 2awl 2awm 2b3p 2b3q 2due 2duf 2dug 2duh 2dui 2emd 2emn 2emo 2fwq 2fzu 2g16 2g2s 2g3d 2g5z 2g6e 2h6v 2h9w 2hcg 2hfc 2hgd 2hgy 2hjo 2hqz 2hrs 2jad 2o24 2o29 2o2b 2okw 2oky 2q57 2q6p 2qrf 2qt2 2qu1 2qz0 2wsn 2wso 2wur 2y0g 2ydz 2ye0 2ye1 2yfp 3cb9 3cbe 3cd1 3cd9 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu 3ed8 3ek4 3ek7 3ek8 3ekh 3ekj 3evp 3evr 3evu 3evv 3g9a 3gex 3gj1 3gj2 3i19 3k1k 3la1 3o77 3o78 3ogo 3osq 3osr 3p28 3sg2 3sg3 3sg4 3sg5 3sg6 3sg7 3sry 3ss0 3ssh 3ssk 3ssl 3ssp 3sst 3ssv 3ssy 3st0 3sv5 3svb 3svc 3svd 3sve 3u8p 3ufz 3ug0 3v3d 3vht 3w1c 3w1d 3wlc 3wld 3ztf 4anj 4ar7 4as8 4b5y 4bdu 4en1 4eul 4ges 4gf6 4h47 4h48 4ik1 4ik3 4ik4 4ik5 4ik8 4ik9 4j89 4j8a 4jfg 4jrb 4ka9 4kag 4kex 4kf5 4kw4 4kw8 4kw9 4l12 4l13 4l1i 4lqt 4lqu 4lw5 4n3d 4ndj 4ndk 4ogs 4orn 4p1q 4p7h 4pa0 4pfe 4u2v 4xbi 4xgy 4xl5 4xov 4xow 4xvp 4z4k 4z4m 4zf3 4zf4 4zf5 5aqb 5dpg 5dph 5dpi 5dpj 5dqb 5dqm 5drf 5drg 5dtx 5dty 5dtz 5du0 5ehu 5f9g 5fgu 5fji 5hbd 5hge 5hw9 5hzo 5j2o 5j3n 5ktg 5t3i

(-) Related Entries Specified in the PDB File

4j89 4j8a