3K9S - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PEROXIDE-BOUND MANGANESE SUPEROXIDE DISMUTASE.

Authors :   J. C. Porta, A. Vahedi-Faridi, G. E. O. Borgstahl

Date :   16 Oct 09 (Deposition) - 12 May 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Manganese Superoxide Dismutase, Peroxide-Bound, Manganese, Metal- Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Porta, A. Vahedi-Faridi, G. E. Borgstahl
Structural Analysis Of Peroxide-Soaked Mnsod Crystals Reveals Side-On Binding Of Peroxide To Active-Site Manganese.
J. Mol. Biol. V. 399 377 2010
PubMed-ID: 20417642 | Reference-DOI: 10.1016/J.JMB.2010.04.031

Molecule 1 - SUPEROXIDE DISMUTASE [MN]
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTTQA10
	Expression System Strain	:	OX326A.1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B3908, JW3879, SODA
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	MNSOD

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION
2	PEO	3	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	PEO	1	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:81 , ASP A:167 , HIS A:171 , HOH A:207 , HOH A:208	BINDING SITE FOR RESIDUE MN A 206
2	AC2	SOFTWARE	HIS B:26 , HIS B:81 , ASP B:167 , HIS B:171 , PEO B:207 , HOH B:208	BINDING SITE FOR RESIDUE MN B 206
3	AC3	SOFTWARE	TYR B:34 , HIS B:81 , GLN B:146 , ASP B:167 , TRP B:169 , HIS B:171 , MN B:206 , HOH B:208	BINDING SITE FOR RESIDUE PEO B 207
4	AC4	SOFTWARE	HIS C:26 , HIS C:81 , ASP C:167 , HIS C:171 , PEO C:207 , HOH C:208 , HOH C:209	BINDING SITE FOR RESIDUE MN C 206
5	AC5	SOFTWARE	HIS C:81 , TRP C:128 , GLN C:146 , ASP C:167 , TRP C:169 , HIS C:171 , MN C:206 , HOH C:208 , HOH C:209	BINDING SITE FOR RESIDUE PEO C 207
6	AC6	SOFTWARE	HIS D:26 , HIS D:81 , ASP D:167 , HIS D:171 , PEO D:208 , HOH D:209	BINDING SITE FOR RESIDUE MN D 206
7	AC7	SOFTWARE	TYR D:34 , HIS D:81 , GLN D:146 , ASP D:167 , TRP D:169 , HIS D:171 , MN D:206 , HOH D:209	BINDING SITE FOR RESIDUE PEO D 208

(no "SS Bond" information available for 3K9S)

Asymmetric Unit

No.	Residues
1	Glu A:15	-	Pro A:16
2	Glu B:15	-	Pro B:16
3	Glu C:15	-	Pro C:16
4	Glu D:15	-	Pro D:16

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SODM_ECOLI_001 *	M	165	L	SODM_ECOLI	---	---	A/B/C/D	M	164	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SODM_ECOLI_001 *	M	165	L	SODM_ECOLI	---	---	A/B	M	164	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SODM_ECOLI_001 *	M	165	L	SODM_ECOLI	---	---	C/D	M	164	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_ECOLI	168-175	4	A:167-174 B:167-174 C:167-174 D:167-174

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_ECOLI	168-175	2	A:167-174 B:167-174 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_ECOLI	168-175	2	- - C:167-174 D:167-174

(no "Exon" information available for 3K9S)

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:205
 aligned with SODM_ECOLI | P00448 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           SODM_ECOLI     2 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 206
               SCOP domains d3k9sa1 A:1-90 Mn superoxide dismutase (MnSOD)                                            d3k9sa2 A:91-205 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k9s A   1 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with SODM_ECOLI | P00448 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           SODM_ECOLI     2 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 206
               SCOP domains d3k9sb1 B:1-90 Mn superoxide dismutase (MnSOD)                                            d3k9sb2 B:91-205 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh...eeeeeee....eeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k9s B   1 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:PROTEIN  Length:205
 aligned with SODM_ECOLI | P00448 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           SODM_ECOLI     2 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 206
               SCOP domains d3k9sc1 C:1-90 Mn superoxide dismutase (MnSOD)                                            d3k9sc2 C:91-205 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k9s C   1 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:205
 aligned with SODM_ECOLI | P00448 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           SODM_ECOLI     2 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 206
               SCOP domains d3k9sd1 D:1-90 Mn superoxide dismutase (MnSOD)                                            d3k9sd2 D:91-205 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Fe_N-3k9sD05 D:1-89                                                                  --Sod_Fe_C-3k9sD01 D:92-201                                                                                     ---- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-3k9sD06 D:1-89                                                                  --Sod_Fe_C-3k9sD02 D:92-201                                                                                     ---- Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-3k9sD07 D:1-89                                                                  --Sod_Fe_C-3k9sD03 D:92-201                                                                                     ---- Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-3k9sD08 D:1-89                                                                  --Sod_Fe_C-3k9sD04 D:92-201                                                                                     ---- Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k9s D   1 SYTLPSLPYAYDALEPHFDKQTMEIHHTKHHQTYVNNANAALESLPEFANLPVEELITKLDQLPADKKTVLRNNAGGHANHSLFWKGLKKGTTLQGDLKAAIERDFGSVDNFKAEFEKAAASRFGSGWAWLVLKGDKLAVVSTANQDSPLMGEAISGASGFPIMGLDVWEHAYYLKFQNRRPDYIKEFWNVVNWDEAAARFAAKK 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ 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 '\|'

(no "CATH Domain" information available for 3K9S)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sod_Fe_C] (46)

Family: Sod_Fe_C (46)

Escherichia coli (strain K12) (7)

1a	Sod_Fe_C-3k9sD01	D:92-201
1b	Sod_Fe_C-3k9sD02	D:92-201
1c	Sod_Fe_C-3k9sD03	D:92-201
1d	Sod_Fe_C-3k9sD04	D:92-201

Clan: no clan defined [family: Sod_Fe_N] (46)

Family: Sod_Fe_N (46)

Escherichia coli (strain K12) (7)

2a	Sod_Fe_N-3k9sD05	D:1-89
2b	Sod_Fe_N-3k9sD06	D:1-89
2c	Sod_Fe_N-3k9sD07	D:1-89
2d	Sod_Fe_N-3k9sD08	D:1-89

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SODM_ECOLI | P00448)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	GO:0071291	cellular response to selenium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from selenium ion.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0010447	response to acidic pH	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu B:15 - Pro B:16	[ RasMol ]
		Glu C:15 - Pro C:16	[ RasMol ]
		Glu D:15 - Pro D:16	[ RasMol ]

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Access by PDB/NDB ID
	3k9s
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	1.15.1.1
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	SODM_ECOLI \| P00448	:	1d5n 1en4 1en5 1en6 1i08 1i0h 1ix9 1ixb 1mmm 1vew 1zlz 3ot7

(no "Related Entries Specified in the PDB File" available for 3K9S)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (1, 4)

Exons (0, 0)

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