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Title :   X-RAY STRUCTURE OF CHEMICALLY ENGINEERED MYCOBACTERIUM TUBERCULOSIS DODECIN

Authors :   X. Vinzenz, W. Grosse, U. Linne, B. Meissner, L. -O. Essen

Date :   17 May 11 (Deposition) - 12 Oct 11 (Release) - 12 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Flavoprotein, Flavin Binding Protein, Protein-Engineering, Putative Storage Protein, Dodecin Hybrid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Vinzenz, W. Grosse, U. Linne, B. Meissner, L. -O. Essen
Chemical Engineering Of Mycobacterium Tuberculosis Dodecin Hybrids.
Chem. Commun. (Camb. ) V. 47 11071 2011
PubMed-ID: 21897938 | Reference-DOI: 10.1039/C1CC12929E

Molecule 1 - DODECIN
	Atcc	:	25618
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-70
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Other Details	:	CYS 59 COVALENTLY MODIFIED WITH N-(2-ETHYL-IODO- ACETAMIDE)-DANSYL
	Strain	:	H37RV

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 23)

No.	Name	Count	Type	Full Name
1	420	6	Ligand/Ion	N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	COA	6	Ligand/Ion	COENZYME A
4	FMN	6	Ligand/Ion	FLAVIN MONONUCLEOTIDE
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 40)

No.	Name	Count	Type	Full Name
1	420	12	Ligand/Ion	N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	COA	12	Ligand/Ion	COENZYME A
4	FMN	12	Ligand/Ion	FLAVIN MONONUCLEOTIDE
5	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:9 , VAL A:11 , GLN A:42 , SER A:43 , ARG A:45 , CYS A:59 , TRP D:38 , GLU D:40 , LYS D:61 , FMN D:300	BINDING SITE FOR RESIDUE 420 A 100
02	AC2	SOFTWARE	ARG A:28 , THR A:32 , MET A:33 , ARG A:34 , PHE A:64 , ARG A:65 , GLU A:67 , HOH A:2030 , ARG D:6 , ILE D:8 , MET D:33 , PHE D:64 , LEU D:66 , COA D:200 , ARG F:6 , LEU F:66 , COA F:200	BINDING SITE FOR RESIDUE COA A 200
03	AC3	SOFTWARE	TYR A:5 , ASP A:37 , TRP A:38 , ARG A:65 , HIS B:3 , ARG B:45 , HIS B:47 , GLN B:57 , ARG B:65 , 420 B:100 , FMN C:300 , VAL F:11 , GLN F:57 , 420 F:100	BINDING SITE FOR RESIDUE FMN A 300
04	AC4	SOFTWARE	GLU A:40 , FMN A:300 , GLU B:9 , VAL B:11 , GLN B:42 , SER B:43 , ARG B:45 , GLN B:57 , CYS B:59 , HOH B:2023 , GLU C:40 , FMN C:300 , ARG F:45 , 420 F:100 , TRP C:38	BINDING SITE FOR RESIDUE 420 B 100
05	AC5	SOFTWARE	ARG B:28 , THR B:32 , ARG B:34 , PHE B:64 , ARG B:65 , GLU B:67 , CL B:1071 , HOH B:2024 , ARG C:6 , ALA C:29 , MET C:33 , LEU C:66 , COA C:200 , ARG E:6 , COA E:200 , MET B:33	BINDING SITE FOR RESIDUE COA B 200
06	AC6	SOFTWARE	TYR B:5 , ASP B:37 , TRP B:38 , ARG B:65 , HOH B:2016 , ARG D:45 , HIS D:47 , GLN D:57 , GLN E:57 , 420 E:100 , FMN F:300	BINDING SITE FOR RESIDUE FMN B 300
07	AC7	SOFTWARE	GLU C:9 , VAL C:11 , GLN C:42 , SER C:43 , ARG C:45 , CYS C:59 , HOH C:2024 , TRP E:38 , LYS E:61 , FMN E:300	BINDING SITE FOR RESIDUE 420 C 100
08	AC8	SOFTWARE	ARG B:6 , LEU B:66 , COA B:200 , CL B:1071 , ARG C:28 , THR C:32 , ARG C:34 , PHE C:64 , ARG C:65 , GLU C:67 , HOH C:2026 , ARG E:6 , ILE E:8 , MET E:33 , PHE E:64 , LEU E:66 , COA E:200	BINDING SITE FOR RESIDUE COA C 200
09	AC9	SOFTWARE	FMN A:300 , VAL B:11 , GLN B:57 , 420 B:100 , TYR C:5 , ASP C:37 , TRP C:38 , ARG C:65 , HOH C:2027 , ARG F:45 , HIS F:47 , GLN F:57 , 420 F:100	BINDING SITE FOR RESIDUE FMN C 300
10	BC1	SOFTWARE	GLU D:9 , VAL D:11 , GLN D:42 , SER D:43 , ARG D:45 , GLN D:57 , CYS D:59 , ARG E:45 , 420 E:100 , TRP F:38 , LYS F:61 , FMN F:300	BINDING SITE FOR RESIDUE 420 D 100
11	BC2	SOFTWARE	ARG A:6 , COA A:200 , ASP C:16 , ARG D:28 , THR D:32 , MET D:33 , ARG D:34 , PHE D:64 , ARG D:65 , GLU D:67 , HOH D:2026 , HOH D:2031 , ARG F:6 , MET F:33 , PHE F:64 , LEU F:66 , COA F:200	BINDING SITE FOR RESIDUE COA D 200
12	BC3	SOFTWARE	ARG A:45 , HIS A:47 , GLN A:57 , 420 A:100 , TYR D:5 , ASP D:37 , TRP D:38 , ARG D:65	BINDING SITE FOR RESIDUE FMN D 300
13	BC4	SOFTWARE	TRP B:38 , GLU B:40 , GLN B:42 , LYS B:61 , FMN B:300 , ARG D:45 , 420 D:100 , GLU E:9 , VAL E:11 , GLN E:42 , SER E:43 , ARG E:45 , GLN E:57 , CYS E:59 , FMN F:300	BINDING SITE FOR RESIDUE 420 E 100
14	BC5	SOFTWARE	ARG B:6 , MET B:33 , LEU B:66 , COA B:200 , CL B:1071 , ARG C:6 , COA C:200 , ARG E:28 , THR E:32 , MET E:33 , ARG E:34 , PHE E:64 , ARG E:65 , GLU E:67 , HOH E:2022	BINDING SITE FOR RESIDUE COA E 200
15	BC6	SOFTWARE	ARG C:45 , GLY C:46 , HIS C:47 , GLN C:57 , 420 C:100 , TYR E:5 , ASP E:37 , TRP E:38	BINDING SITE FOR RESIDUE FMN E 300
16	BC7	SOFTWARE	VAL A:7 , TRP A:38 , LYS A:61 , FMN A:300 , ARG B:45 , HIS B:47 , 420 B:100 , FMN C:300 , GLU F:9 , VAL F:11 , GLN F:42 , SER F:43 , ARG F:45 , GLN F:57 , CYS F:59	BINDING SITE FOR RESIDUE 420 F 100
17	BC8	SOFTWARE	ARG A:6 , ILE A:8 , MET A:33 , PHE A:64 , LEU A:66 , COA A:200 , ARG D:6 , LEU D:66 , COA D:200 , HOH D:2028 , ARG F:28 , THR F:32 , MET F:33 , ARG F:34 , PHE F:64 , ARG F:65 , GLU F:67 , HOH F:2022 , HOH F:2024 , HOH F:2025	BINDING SITE FOR RESIDUE COA F 200
18	BC9	SOFTWARE	FMN B:300 , ARG D:45 , GLN D:57 , 420 D:100 , ARG E:45 , HIS E:47 , GLN E:57 , 420 E:100 , HIS F:3 , TYR F:5 , ASP F:37 , ASP F:50 , ARG F:65 , TRP F:38	BINDING SITE FOR RESIDUE FMN F 300
19	CC1	SOFTWARE	LYS A:61 , LYS F:61	BINDING SITE FOR RESIDUE CL A1070
20	CC2	SOFTWARE	LYS B:61 , LYS C:61 , LYS E:61	BINDING SITE FOR RESIDUE CL B1070
21	CC3	SOFTWARE	COA B:200 , COA C:200 , COA E:200	BINDING SITE FOR RESIDUE CL B1071
22	CC4	SOFTWARE	ARG A:6 , VAL A:7 , ILE A:8 , GLU A:9 , HOH A:2006 , ARG D:6 , VAL D:7 , ILE D:8 , GLU D:9 , HOH D:2005 , ARG F:6 , VAL F:7 , ILE F:8 , GLU F:9	BINDING SITE FOR RESIDUE SO4 D1070
23	CC5	SOFTWARE	ARG B:6 , VAL B:7 , ILE B:8 , GLU B:9 , HOH B:2003 , ARG C:6 , VAL C:7 , ILE C:8 , GLU C:9 , HOH C:2002 , ARG E:6 , VAL E:7 , ILE E:8 , GLU E:9	BINDING SITE FOR RESIDUE SO4 E1070

(no "SS Bond" information available for 2YJ0)

(no "Cis Peptide Bond" information available for 2YJ0)

(no "SAP(SNP)/Variant" information available for 2YJ0)

(no "PROSITE Motif" information available for 2YJ0)

(no "Exon" information available for 2YJ0)

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:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yj0a_ A: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yj0 A  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLED 68
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:67
                                    12        22        32        42        52        62       
          Q8VK10_MYCTO    3 NHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yj0b_ B: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2yj0 B  2 NHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLED 68
                                    11        21        31        41        51        61

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yj0c_ C: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yj0 C  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLED 68
                                    10        20        30        40        50        60

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yj0d_ D: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yj0 D  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLED 68
                                    10        20        30        40        50        60

Chain E from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yj0e_ E: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yj0 E  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLED 68
                                    10        20        30        40        50        60

Chain F from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yj0f_ F: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yj0 F  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLED 68
                                    10        20        30        40        50        60

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Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Dodecin subunit-like (56)

Superfamily: Dodecin-like (33)

Family: automated matches (4)

Protein domain: automated matches (4)

Mycobacterium tuberculosis [TaxId: 83332] (2)

1a	d2yj0a_	A:
1b	d2yj0b_	B:
1c	d2yj0c_	C:
1d	d2yj0d_	D:
1e	d2yj0e_	E:
1f	d2yj0f_	F:

(no "CATH Domain" information available for 2YJ0)

(no "Pfam Domain" information available for 2YJ0)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q8VK10_MYCTO | Q8VK10)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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	Q8VK10_MYCTO \| Q8VK10	:	2yiz 3oqt

2yiz	X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DODECIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 23)

Sites (23, 23)

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

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SCOP Domains (1, 6)

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Gene Ontology (2, 2)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File