4FZL - JenaLib

Title :   HIGH RESOLUTION STRUCTURE OF TRUNCATED BACTERIOCIN SYRINGACIN M FROM PSEUDOMONAS SYRINGAE PV. TOMATO DC3000

Authors :   A. W. Roszak, R. Grinter, J. R. Cogdell, D. Walker

Date :   06 Jul 12 (Deposition) - 03 Oct 12 (Release) - 28 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.46

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Phosphatase, Calcium Binding, Lipid Ii Binding, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Grinter, A. W. Roszak, R. J. Cogdell, J. J. Milner, D. Walker
The Crystal Structure Of The Lipid Ii-Degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships Between Colicin M-Like Bacteriocins.
J. Biol. Chem. V. 287 38876 2012
PubMed-ID: 22995910 | Reference-DOI: 10.1074/JBC.M112.400150

Compounds

Molecule 1 - BACTERIOCIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETMDC
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET21A
	Fragment	:	UNP RESIDUES 38-276
	Gene	:	PSPTO_0572
	Organism Scientific	:	PSEUDOMONAS SYRINGAE PV. TOMATO
	Organism Taxid	:	223283
	Strain	:	DC3000

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 18)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:202 , ASN A:204 , ASP A:232 , EDO A:302 , HOH A:427 , HOH A:436	BINDING SITE FOR RESIDUE CA A 301
02	AC2	SOFTWARE	ASN A:204 , ASP A:232 , VAL A:233 , CA A:301 , HOH A:427 , HOH A:436	BINDING SITE FOR RESIDUE EDO A 302
03	AC3	SOFTWARE	ARG A:208 , ARG A:228 , ALA A:229 , PHE A:230 , HOH A:581	BINDING SITE FOR RESIDUE EDO A 303
04	AC4	SOFTWARE	ARG A:208	BINDING SITE FOR RESIDUE EDO A 304
05	AC5	SOFTWARE	LEU A:183 , ASP A:184 , VAL A:185 , HOH A:419	BINDING SITE FOR RESIDUE EDO A 305
06	AC6	SOFTWARE	ASN A:159 , VAL A:160 , ASP A:161 , HOH A:517	BINDING SITE FOR RESIDUE EDO A 306
07	AC7	SOFTWARE	PRO A:257 , PHE A:258	BINDING SITE FOR RESIDUE EDO A 307
08	AC8	SOFTWARE	GLN A:112 , ILE A:113 , ASN A:114 , HOH A:678 , ILE B:74 , EDO B:304	BINDING SITE FOR RESIDUE CL A 308
09	AC9	SOFTWARE	TYR A:189 , ASP A:190 , HOH A:691	BINDING SITE FOR RESIDUE EDO A 309
10	BC1	SOFTWARE	LEU B:202 , ASN B:204 , ASP B:232 , EDO B:303 , HOH B:439 , HOH B:516	BINDING SITE FOR RESIDUE CA B 301
11	BC2	SOFTWARE	ASP B:214 , EDO B:308 , HOH B:522 , HOH B:528 , HOH B:529	BINDING SITE FOR RESIDUE MG B 302
12	BC3	SOFTWARE	ASN B:204 , ASP B:232 , VAL B:233 , CA B:301 , HOH B:439 , HOH B:441 , HOH B:516	BINDING SITE FOR RESIDUE EDO B 303
13	BC4	SOFTWARE	GLN A:112 , ASN A:114 , CL A:308 , HOH A:460 , GLY B:73 , LYS B:77 , GLU B:115 , HOH B:649	BINDING SITE FOR RESIDUE EDO B 304
14	BC5	SOFTWARE	ARG B:208 , ARG B:228 , ALA B:229 , HOH B:527	BINDING SITE FOR RESIDUE EDO B 305
15	BC6	SOFTWARE	ASP B:214 , ASN B:216 , ALA B:220 , TRP B:221 , THR B:222	BINDING SITE FOR RESIDUE EDO B 306
16	BC7	SOFTWARE	THR B:212 , THR B:222 , SER B:224 , HOH B:599	BINDING SITE FOR RESIDUE EDO B 307
17	BC8	SOFTWARE	THR B:180 , ASP B:214 , MG B:302 , HOH B:528 , HOH B:529	BINDING SITE FOR RESIDUE EDO B 308
18	BC9	SOFTWARE	ILE A:74 , GLN B:112 , ILE B:113 , ASN B:114	BINDING SITE FOR RESIDUE CL B 309

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhh.............hhhhhhhhhhhhh....ee.hhhhhh...hhhhhhhhhhhhh.....eeeeeeeeeeee.hhhhhhhhhhhheeeeeeeeeeee.....eeeeeeeee..eee..hhhhhhhhhhhhhhhhhh......eeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fzl A  38 GMQNPVATVLLLQGDLYCSPNCLATFQDQARRDSFGIQSKVALKTFAAADQREAEGRDLRTAYNEIATDIGRSQQINENIIKYPPGNHVLSGGLMTPFHALAHGMFGLGAPLTFPIQNVGLNVDIRGIPDVMNVIQSARPVGTSSLDVNFAYDVGKDSNASWLTLGNITLRLVGTIDKNASGAWTFSGEIRAFNDVYDANPSNHRGWLGENLTSLLSAVPFTSYSIEIPGSLPVTVSGN 276
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267

Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhh.............hhhhhhhhhhhhh....ee.hhhhh....hhhhhhhhhhhhhhh...eeeeeeeeeeee.hhhhhhhhhhhheeeeeeeeeeee....eeeeeeeeee..eee..hhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fzl B  39 MQNPVATVLLLQGDLYCSPNCLATFQDQARRDSFGIQSKVALKTFAAADQREAEGRDLRTAYNEIATDIGRSQQINENIIKYPPGNHVLSGGLMTPFHALAHGMFGLGAPLTFPIQNVGLNVDIRGIPDVMNVIQSARPVGTSSLDVNFAYDVGKDSNASWLTLGNITLRLVGTIDKNASGAWTFSGEIRAFNDVYDANPSNHRGWLGENLTSLLSAVPFTSYSIEIPGSLPVTVSGNLEHH 280
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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