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(-) Description

Title :  CRYSTAL STRUCTURE OF PECTOCIN M2 AT 1.86 ANGSTROMS
 
Authors :  R. Grinter, A. W. Roszak, K. Zeth, C. J. Cogdell, D. Walker
Date :  09 Oct 13  (Deposition) - 04 Jun 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (2x)
Biol. Unit 4:  B  (2x)
Keywords :  Plant-Like Ferredoxin, Colicin M-Like Cytotoxic Domain, Lipid-Ii Hydrolase, Bacteriocin, Protein Antibiotc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Grinter, I. Josts, K. Zeth, A. W. Roszak, L. C. Mccaughey, R. J. Cogdell, J. J. Milner, S. M. Kelly, O. Byron, D. Walker
Structure Of The Atypical Bacteriocin Pectocin M2 Implies A Novel Mechanism Of Protein Uptake.
Mol. Microbiol. V. 93 234 2014
PubMed-ID: 24865810  |  Reference-DOI: 10.1111/MMI.12655

(-) Compounds

Molecule 1 - PECTOCIN M2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PECTOBACTERIUM CAROTOVORUM SUBSP. BRASILIENSIS PBR1692
    Organism Taxid: 558269
    Strain: PBR1692

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): A 
Biological Unit 4 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 66)

Asymmetric Unit (5, 66)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL35Ligand/IonGLYCEROL
4MPD10Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO418Ligand/IonSULFATE ION
Biological Unit 1 (4, 30)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL15Ligand/IonGLYCEROL
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO48Ligand/IonSULFATE ION
Biological Unit 2 (4, 35)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL20Ligand/IonGLYCEROL
4MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO410Ligand/IonSULFATE ION
Biological Unit 3 (4, 60)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL30Ligand/IonGLYCEROL
4MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO416Ligand/IonSULFATE ION
Biological Unit 4 (4, 70)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL40Ligand/IonGLYCEROL
4MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO420Ligand/IonSULFATE ION

(-) Sites  (66, 66)

Asymmetric Unit (66, 66)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:37 , CYS A:38 , ARG A:39 , GLY A:41 , ALA A:42 , CYS A:43 , CYS A:46 , CYS A:75BINDING SITE FOR RESIDUE FES A 301
02AC2SOFTWARESER A:64 , GLU A:65 , HOH A:497BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREGLY A:189 , TYR A:190 , ASN A:248 , ASN A:249 , GOL A:322 , MPD A:330 , HOH A:471BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREARG A:258 , HOH A:426BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWARESER A:179 , ASP A:180 , GOL A:318 , HOH A:528 , HOH A:617 , ASN B:268BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREARG A:39 , SO4 B:307 , HOH B:576BINDING SITE FOR RESIDUE SO4 A 306
07AC7SOFTWAREPHE A:153 , ASN A:154 , ILE A:155 , LYS A:264BINDING SITE FOR RESIDUE SO4 A 307
08AC8SOFTWAREASN A:147 , ASN A:149 , GLY A:261 , GLU A:262 , HOH A:427BINDING SITE FOR RESIDUE SO4 A 308
09AC9SOFTWAREHOH A:630BINDING SITE FOR RESIDUE SO4 A 309
10BC1SOFTWARETHR A:227 , TYR A:228 , ASP A:229 , HOH A:445 , HOH A:587 , HOH A:626BINDING SITE FOR RESIDUE GOL A 310
11BC2SOFTWARETYR A:4 , SER A:81 , ASP A:82 , HOH A:562 , HOH A:563BINDING SITE FOR RESIDUE GOL A 311
12BC3SOFTWARETHR A:10 , LEU A:34 , PRO A:35 , THR A:87 , GLY A:88 , LYS A:210 , SER A:211 , MPD A:325 , MPD A:327BINDING SITE FOR RESIDUE GOL A 312
13BC4SOFTWARETYR A:36 , SER A:45 , GLU A:90 , GLY A:173 , ARG A:174 , GOL A:314 , MPD A:327 , HOH A:499 , HOH A:549 , HOH A:628BINDING SITE FOR RESIDUE GOL A 313
14BC5SOFTWARELEU A:34 , PRO A:35 , TYR A:36 , LYS A:170 , ASN A:171 , VAL A:172 , GOL A:313 , GOL B:326BINDING SITE FOR RESIDUE GOL A 314
15BC6SOFTWARETYR A:136 , ASP A:229 , ASN A:231 , GLY A:252 , PRO A:254 , HOH A:575BINDING SITE FOR RESIDUE GOL A 315
16BC7SOFTWARELEU A:247 , ASN A:248 , LEU A:250 , SER A:251 , HOH A:623BINDING SITE FOR RESIDUE GOL A 316
17BC8SOFTWAREASN A:198 , ILE A:199 , THR A:200 , ASP A:226 , HOH A:442 , HOH A:619BINDING SITE FOR RESIDUE GOL A 317
18BC9SOFTWAREASP A:180 , SO4 A:305BINDING SITE FOR RESIDUE GOL A 318
19CC1SOFTWAREARG A:222 , SER A:223 , TYR A:224 , GOL A:320 , GOL A:324 , HOH A:616BINDING SITE FOR RESIDUE GOL A 319
20CC2SOFTWARETYR A:224 , ASN A:225 , GOL A:319 , GOL A:323 , HOH A:439BINDING SITE FOR RESIDUE GOL A 320
21CC3SOFTWAREHOH A:594 , HOH A:597 , LYS B:21 , LYS B:29BINDING SITE FOR RESIDUE GOL A 321
22CC4SOFTWAREPHE A:97 , GLU A:98 , GLY A:189 , TYR A:190 , SER A:191 , SO4 A:303BINDING SITE FOR RESIDUE GOL A 322
23CC5SOFTWAREGOL A:320 , HOH A:439 , HOH A:470BINDING SITE FOR RESIDUE GOL A 323
24CC6SOFTWAREGOL A:319BINDING SITE FOR RESIDUE GOL A 324
25CC7SOFTWARETHR A:10 , THR A:11 , LYS A:210 , SER A:211 , ASP A:212 , GOL A:312BINDING SITE FOR RESIDUE MPD A 325
26CC8SOFTWAREHOH A:425BINDING SITE FOR RESIDUE MPD A 326
27CC9SOFTWAREGLY A:88 , ASP A:91 , GOL A:312 , GOL A:313 , HOH A:461 , HOH A:610 , HOH A:628BINDING SITE FOR RESIDUE MPD A 327
28DC1SOFTWARETRP A:215 , LYS A:270 , LYS A:271 , HOH A:510 , ASP B:176 , HOH B:501BINDING SITE FOR RESIDUE MPD A 328
29DC2SOFTWAREASN A:33 , VAL A:172 , LYS A:210 , SER A:211 , GLY A:213 , LYS A:271BINDING SITE FOR RESIDUE MPD A 329
30DC3SOFTWAREALA A:186 , SO4 A:303 , TYR B:36 , ARG B:39BINDING SITE FOR RESIDUE MPD A 330
31DC4SOFTWAREGLY A:169 , LYS A:170BINDING SITE FOR RESIDUE CL A 331
32DC5SOFTWARESER B:37 , CYS B:38 , ARG B:39 , GLY B:41 , ALA B:42 , CYS B:43 , CYS B:46 , CYS B:75BINDING SITE FOR RESIDUE FES B 301
33DC6SOFTWAREASN A:268 , SER B:179 , ASP B:180 , SO4 B:308 , HOH B:506 , HOH B:507BINDING SITE FOR RESIDUE SO4 B 302
34DC7SOFTWAREARG B:258 , HOH B:431 , HOH B:432BINDING SITE FOR RESIDUE SO4 B 303
35DC8SOFTWAREPHE B:153 , ASN B:154 , ILE B:155BINDING SITE FOR RESIDUE SO4 B 304
36DC9SOFTWAREASN B:147 , ASN B:149 , GLY B:261 , GLU B:262 , GOL B:325 , HOH B:515BINDING SITE FOR RESIDUE SO4 B 305
37EC1SOFTWAREPHE B:130 , HOH B:451BINDING SITE FOR RESIDUE SO4 B 306
38EC2SOFTWARESO4 A:306 , GLY B:189 , TYR B:190 , ASN B:248 , ASN B:249 , GOL B:327 , HOH B:477 , HOH B:576BINDING SITE FOR RESIDUE SO4 B 307
39EC3SOFTWARESO4 B:302BINDING SITE FOR RESIDUE SO4 B 308
40EC4SOFTWARESER B:61 , PHE B:62 , LEU B:63 , SER B:64 , GOL B:321 , GOL B:324 , HOH B:599BINDING SITE FOR RESIDUE SO4 B 309
41EC5SOFTWAREGLY B:120 , GLU B:143 , SER B:145 , ARG B:258BINDING SITE FOR RESIDUE SO4 B 310
42EC6SOFTWAREGLN B:216 , LYS B:266 , HOH B:607BINDING SITE FOR RESIDUE SO4 B 311
43EC7SOFTWAREHOH B:429BINDING SITE FOR RESIDUE GOL B 312
44EC8SOFTWARETHR B:227 , TYR B:228 , ASP B:229 , ARG B:236 , HOH B:450 , HOH B:454BINDING SITE FOR RESIDUE GOL B 313
45EC9SOFTWARELEU B:34 , PRO B:35 , TYR B:36 , LYS B:170 , ASN B:171 , VAL B:172 , GOL B:323BINDING SITE FOR RESIDUE GOL B 314
46FC1SOFTWARETHR B:87 , GLY B:88 , LYS B:92 , GOL B:316BINDING SITE FOR RESIDUE GOL B 315
47FC2SOFTWARELYS B:92 , GOL B:315BINDING SITE FOR RESIDUE GOL B 316
48FC3SOFTWARELYS B:92 , LEU B:94 , ASN B:249 , LEU B:250 , SER B:251 , GOL B:318BINDING SITE FOR RESIDUE GOL B 317
49FC4SOFTWARELEU B:247 , ASN B:248 , LEU B:250 , GOL B:317 , HOH B:503BINDING SITE FOR RESIDUE GOL B 318
50FC5SOFTWAREGLY B:53 , GLU B:54 , VAL B:55 , GLU B:68 , LYS B:69 , GOL B:320 , HOH B:597 , HOH B:598BINDING SITE FOR RESIDUE GOL B 319
51FC6SOFTWARESER B:52 , GLY B:53 , GOL B:319 , HOH B:562BINDING SITE FOR RESIDUE GOL B 320
52FC7SOFTWAREGLU B:65 , SO4 B:309 , HOH B:497BINDING SITE FOR RESIDUE GOL B 321
53FC8SOFTWARESER B:45 , GLU B:90 , ASP B:91 , GOL B:323BINDING SITE FOR RESIDUE GOL B 322
54FC9SOFTWARETYR B:36 , SER B:45 , GLU B:90 , GLY B:173 , ARG B:174 , GOL B:314 , GOL B:322BINDING SITE FOR RESIDUE GOL B 323
55GC1SOFTWARESER B:64 , GLU B:95 , ASP B:96 , SO4 B:309 , HOH B:545BINDING SITE FOR RESIDUE GOL B 324
56GC2SOFTWAREASN B:147 , ASP B:150 , SO4 B:305BINDING SITE FOR RESIDUE GOL B 325
57GC3SOFTWAREGOL A:314 , ASN B:156 , SER B:158 , MPD B:332 , HOH B:606BINDING SITE FOR RESIDUE GOL B 326
58GC4SOFTWAREASP B:188 , GLY B:189 , TYR B:190 , SER B:191 , VAL B:192 , SO4 B:307 , HOH B:577BINDING SITE FOR RESIDUE GOL B 327
59GC5SOFTWAREASN B:198 , ILE B:199 , THR B:200 , ASP B:226 , HOH B:447 , HOH B:473BINDING SITE FOR RESIDUE GOL B 328
60GC6SOFTWAREVAL B:206 , ASN B:208 , GLN B:216 , GLU B:218 , HOH B:527BINDING SITE FOR RESIDUE GOL B 329
61GC7SOFTWARETYR B:224 , ASN B:225 , GOL B:331 , MPD B:333BINDING SITE FOR RESIDUE GOL B 330
62GC8SOFTWAREARG B:222 , SER B:223 , TYR B:224 , GOL B:330 , HOH B:468 , HOH B:516BINDING SITE FOR RESIDUE GOL B 331
63GC9SOFTWAREASP A:176 , MET B:164 , GOL B:326 , HOH B:502 , HOH B:593BINDING SITE FOR RESIDUE MPD B 332
64HC1SOFTWAREASP B:180 , THR B:200 , GOL B:330BINDING SITE FOR RESIDUE MPD B 333
65HC2SOFTWARELYS B:70 , ALA B:102 , ARG B:118 , HOH B:445 , HOH B:521BINDING SITE FOR RESIDUE MPD B 334
66HC3SOFTWARETHR B:10 , THR B:11 , LYS B:210 , SER B:211 , ASP B:212 , HOH B:519 , HOH B:549 , HOH B:568BINDING SITE FOR RESIDUE MPD B 335

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N58)

(-) Exons   (0, 0)

(no "Exon" information available for 4N58)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeee...hhhhhhhhh................eeeeee..ee.......hhhhhhheee.hhhee...eeee..hhhhh.hhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhh....ee.hhhhh....hhhhhhhhhhhhh....eeeeeeeeeeee.hhhhhhhhhhhheeeeeeeeeeee....eeeeeeeeee..eee..hhhhh....hhhhhhhhh......eeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n58 A   2 ATYKVKDVTTGAEIEVPDDKYILDEFEKQGVNLPYSCRAGACSSCVALISSGEVDQSDGSFLSEKQEKKYILTCCSYPKSDCTIETGYEDKILEDFEIELAETGLEFFNLPRSGEILSGVTAPFEAFDHYLFGNGVERSININDVGFNINVSQIPPIMSLLNGKNVGRFDIGSDFVRNTALDGYSVAAYLGNITMRTEGVLNVKSDGTWQYEGVIRSYNDTYDANPSTHRGALGEWATGVLNNLSGTPYEIRIPGELKIKENGKKL 272
                                    11        21        31        41        51        61        71        81        91       101       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266      
                                                                                                                                      110|                                                                                                                                                            
                                                                                                                                       116                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee....hhhhhhhhh................eeeeee..ee.........hhhh.eee.hhhee...eeeee.hhhhh.hhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhh....ee.hhhhh....hhhhhhhhhhhhhh...eeeeeeeeeeee.hhhhhhhhhhhheeeeeeeeeeee....eeeeeeeeee..eee..hhhhh...hhhhhhhhhhhh....eeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n58 B   3 TYKVKDVTTGAEIEVPDDKYILDEFEKQGVNLPYSCRAGACSSCVALISSGEVDQSDGSFLSEKQEKKYILTCCSYPKSDCTIETGYEDKILEDFEIELAETGLEFFNLPRSGEILSGVTAPFEAFDHYLFGNGVERSININDVGFNINVSQIPPIMSLLNGKNVGRFDIGSDFVRNTALDGYSVAAYLGNITMRTEGVLNVKSDGTWQYEGVIRSYNDTYDANPSTHRGALGEWATGVLNNLSGTPYEIRIPGELKIKENGKKLE 273
                                    12        22        32        42        52        62        72        82        92       102       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267      
                                                                                                                                     110|                                                                                                                                                             
                                                                                                                                      116
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  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 4N58)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N58)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N58)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4N58)

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  4n58
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  A0A067XG75_P | A0A067XG75
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  A0A067XG75_P | A0A067XG75
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 Related Entries

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

UniProtKB/TrEMBL
        A0A067XG75_P | A0A067XG75: 4n59

(-) Related Entries Specified in the PDB File

2xmx 4fzl 4fzm 4fzn 4g75 4n59