3D4R - JenaLib

Title :   CRYSTAL STRUCTURE OF A DUF2118 FAMILY PROTEIN (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   14 May 08 (Deposition) - 08 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: E,F  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Domain Of Unknown Function From The Pfam-B_34464 Family (Np_987166. 1) From Methanococcus Maripaludis Jj (Dsm 2067) At 2. 20 A Resolution
To Be Published
PubMed: search

Compounds

Molecule 1 - DOMAIN OF UNKNOWN FUNCTION FROM THE PFAM-B_34464 FAMILY
	Atcc	:	43000
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_987166.1, MMP0046
	Mutation	:	YES
	Organism Common	:	ARCHAEA
	Organism Scientific	:	METHANOCOCCUS MARIPALUDIS
	Organism Taxid	:	39152
	Strain	:	JJ [DSM 2067]

Structural Features

Chains, Units

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:					E	F
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 41)

Asymmetric Unit (3, 41)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 15)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU E:104 , TYR E:107 , ARG F:102 , TYR F:107	BINDING SITE FOR RESIDUE EDO F 151
02	AC2	SOFTWARE	ARG C:108 , ASN C:123 , LYS F:115	BINDING SITE FOR RESIDUE EDO C 151
03	AC3	SOFTWARE	ASP A:98 , PHE A:99 , ARG B:102 , GLY B:128 , THR B:129 , GLU B:150	BINDING SITE FOR RESIDUE EDO A 151
04	AC4	SOFTWARE	TYR A:94 , ILE A:96 , ARG A:108 , THR A:111	BINDING SITE FOR RESIDUE EDO A 152
05	AC5	SOFTWARE	TYR B:94 , TYR E:94 , ARG E:108 , THR E:111	BINDING SITE FOR RESIDUE EDO E 151
06	AC6	SOFTWARE	ILE F:3 , GLN F:67 , TYR F:68 , PRO F:69 , LYS F:71	BINDING SITE FOR RESIDUE EDO F 152
07	AC7	SOFTWARE	GLY F:90 , TYR F:91 , LEU F:112 , GLU F:113 , SER F:114 , ASP F:118 , ARG F:120	BINDING SITE FOR RESIDUE EDO F 153
08	AC8	SOFTWARE	ARG C:108 , TYR C:121 , LYS F:116	BINDING SITE FOR RESIDUE EDO C 152
09	AC9	SOFTWARE	ASP C:70 , GLY D:128 , THR D:129 , LEU D:148 , GLU D:149 , GLU D:150	BINDING SITE FOR RESIDUE EDO D 151
10	BC1	SOFTWARE	SER E:127 , GLU E:150 , LYS F:2	BINDING SITE FOR RESIDUE EDO E 152
11	BC2	SOFTWARE	ASP C:98 , PHE C:99 , ARG D:102 , LEU D:104 , GLY D:128 , THR D:129 , GLU D:150	BINDING SITE FOR RESIDUE PEG D 152

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)
	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:158
 aligned with Q6M171_METMP | Q6M171 from UniProtKB/TrEMBL  Length:150

    Alignment length:158
                                    1                                                                                                                                                      
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q6M171_METMP     - --------MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTFTYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.......eeeeehhh.eeee...........eeeeee...hhhh.ee..ee...eeee.....eeeee......eeeee...eeee.....eee....eeeeee.....eeeee....eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4r A  -7 HENLYFQGmKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYmSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPAEGYKVYPImDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFmNEIPSERANYVFYmLEE 150
                                    |2        12        22        32        42        52  |     62        72        82        92    |  102       112       122       132|      142    |   
                                    1-MSE                                                55-MSE                                    97-MSE                             133-MSE       147-MSE

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q6M171_METMP | Q6M171 from UniProtKB/TrEMBL  Length:150

    Alignment length:157
                                   1                                                                                                                                                      
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       
         Q6M171_METMP     - -------MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTFTYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.......eeeeehhh.eeee...........eeeeee....hhh.ee..ee...eeee.....eeeee......eeeeeee.eeee......ee....eeeeee.....eeeee....eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4r B  -6 ENLYFQGmKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYmSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPAEGYKVYPImDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFmNEIPSERANYVFYmLEE 150
                                   | 3        13        23        33        43        53 |      63        73        83        93   |   103       113       123       133       143   |   
                                   1-MSE                                                55-MSE                                    97-MSE                             133-MSE       147-MSE

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with Q6M171_METMP | Q6M171 from UniProtKB/TrEMBL  Length:150

    Alignment length:158
                                    1                                                                                                                                                      
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q6M171_METMP     - --------MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTFTYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.......eeeeehhh.eeeee..........eeeeee...hhhh.ee..ee...eeee.....eeeee......eeeee...eeee.....eee....eeeeee.....eeeee....eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4r C  -7 HENLYFQGmKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYmSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPAEGYKVYPImDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFmNEIPSERANYVFYmLEE 150
                                    |2        12        22        32        42        52  |     62        72        82        92    |  102       112       122       132|      142    |   
                                    1-MSE                                                55-MSE                                    97-MSE                             133-MSE       147-MSE

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with Q6M171_METMP | Q6M171 from UniProtKB/TrEMBL  Length:150

    Alignment length:158
                                    1                                                                                                                                                      
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q6M171_METMP     - --------MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTFTYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..ee..eeeee.......eeeeehhh.eeeee..........eeeeee....hhh.ee..ee...eeee.....eeeee......eeeeeee.eeee......ee....eeeeee.....eeeee....eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4r D  -7 HENLYFQGmKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYmSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPAEGYKVYPImDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFmNEIPSERANYVFYmLEE 150
                                    |2        12        22        32        42        52  |     62        72        82        92    |  102       112       122       132|      142    |   
                                    1-MSE                                                55-MSE                                    97-MSE                             133-MSE       147-MSE

Chain E from PDB  Type:PROTEIN  Length:151
 aligned with Q6M171_METMP | Q6M171 from UniProtKB/TrEMBL  Length:150

    Alignment length:153
                               1                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147   
         Q6M171_METMP     - ---MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTFTYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.......eeeeehhh.eeeee..--......eeeeee...hhhh.ee..ee...eeeee....eeeee......eeeee...eeee.....eee....eeeeee.....eeeee....eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4r E  -2 FQGmKIPKIYVEGELNDGDRVAIEKDGNAIIFLEK--EYSGNGKLLYQVIYDDLAKYmSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPAEGYKVYPImDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFmNEIPSERANYVFYmLEE 150
                               |     7        17        27    |  |37        47       |57        67        77        87        97       107       117       127     | 137       147   
                               1-MSE                         32 35                  55-MSE                                    97-MSE                             133-MSE       147-MSE

Chain F from PDB  Type:PROTEIN  Length:158
 aligned with Q6M171_METMP | Q6M171 from UniProtKB/TrEMBL  Length:150

    Alignment length:158
                                    1                                                                                                                                                      
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142        
         Q6M171_METMP     - --------MKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYMSLDTLKKDVLIQYPDKHTFTYLKAGTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYVFYMLEE 150
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.......eeeeehhh.eeeee..........eeeeee...hhhh.ee..ee...eeee.....eeeee......eeeee...eeee.....eee....eeeeee.....eeeee....eeeeeeee.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4r F  -7 HENLYFQGmKIPKIYVEGELNDGDRVAIEKDGNAIIFLEKDEEYSGNGKLLYQVIYDDLAKYmSLDTLKKDVLIQYPDKHTLTYLKAGTKLISVPAEGYKVYPImDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFmNEIPSERANYVFYmLEE 150
                                    |2        12        22        32        42        52  |     62        72        82        92    |  102       112       122       132|      142    |   
                                    1-MSE                                                55-MSE                                    97-MSE                             133-MSE       147-MSE

Legend:		→ Mismatch	(orange background)
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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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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Description