3D55 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF M. TUBERCULOSIS YEFM ANTITOXIN

Authors :   P. Kumar, B. Issac, E. J. Dodson, J. P. Turkenberg, S. C. Mande

Date :   15 May 08 (Deposition) - 02 Dec 08 (Release) - 02 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x)

Keywords :   Tetramer, Toxin Neutraliser, Toxin Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kumar, B. Issac, E. J. Dodson, J. P. Turkenburg, S. C. Mande
Crystal Structure Of Mycobacterium Tuberculosis Yefm Antitoxin Reveals That It Is Not An Intrinsically Unstructured Protein
J. Mol. Biol. V. 383 482 2008
PubMed-ID: 18793646 | Reference-DOI: 10.1016/J.JMB.2008.08.067
(for further references see the PDB file header)

Molecule 1 - UNCHARACTERIZED PROTEIN RV3357/MT3465
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RV3357, MT3465, MTV004.14
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	ANTITOXIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:57 , ARG A:60 , ARG A:61 , ARG B:60 , ARG B:61 , LYS C:78	BINDING SITE FOR RESIDUE SO4 A 201
2	AC2	SOFTWARE	PHE C:13 , SER D:4 , ALA D:5 , SER D:6 , THR D:29 , SER D:30 , ARG D:31	BINDING SITE FOR RESIDUE SO4 D 202

(no "SS Bond" information available for 3D55)

(no "Cis Peptide Bond" information available for 3D55)

(no "SAP(SNP)/Variant" information available for 3D55)

(no "PROSITE Motif" information available for 3D55)

(no "Exon" information available for 3D55)

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 RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:68
                                    10        20        30        40        50        60        
            RELJ_MYCTO    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
               SCOP domains d3d55a_ A: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3d55 A  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
                                    10        20        30        40        50        60

Chain A from PDB  Type:PROTEIN  Length:68
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:68
                                    10        20        30        40        50        60        
            RELJ_MYCTU    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
               SCOP domains d3d55a_ A: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3d55 A  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            RELJ_MYCTO    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 84
               SCOP domains d3d55b_ B: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhhhhhhhh...eeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3d55 B  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 84
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            RELJ_MYCTU    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 84
               SCOP domains d3d55b_ B: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhhhhhhhh...eeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3d55 B  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 84
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
            RELJ_MYCTO    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
               SCOP domains d3d55c_ C: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  3d55 C  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
            RELJ_MYCTU    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
               SCOP domains d3d55c_ C: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  3d55 C  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
                                    10        20        30        40        50        60        70        80

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
            RELJ_MYCTO    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREMAGG 89
               SCOP domains d3d55d_ D: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhhhhhhhh...eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh..-------hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3d55 D  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAV-------SAFTKSVDELREMAGG 89
                                    10        20        30        40        50        60     |   -   |    80         
                                                                                            66      74

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
            RELJ_MYCTU    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREMAGG 89
               SCOP domains d3d55d_ D: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhhhhhhhh...eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh..-------hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3d55 D  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAV-------SAFTKSVDELREMAGG 89
                                    10        20        30        40        50        60     |   -   |    80         
                                                                                            66      74

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: YefM-like (5)

Superfamily: YefM-like (5)

Family: automated matches (3)

Protein domain: automated matches (3)

Mycobacterium tuberculosis [TaxId: 1773] (3)

1a	d3d55a_	A:
1b	d3d55b_	B:
1c	d3d55c_	C:
1d	d3d55d_	D:

(no "CATH Domain" information available for 3D55)

(no "Pfam Domain" information available for 3D55)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RELJ_MYCTO | P9WF24)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Chain A,B,C,D (RELJ_MYCTU | P9WF25)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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3cto	SAME PROTEIN CRYSTALLIZED UNDER DIFFERENT CRYSTALLIZATION CONDITION

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Ligands, Modified Residues, Ions (1, 2)

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