3H16 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A BACTERIA TIR DOMAIN, PDTIR FROM PARACOCCUS DENITRIFICANS

Authors :   S. L. Chan, L. Y. Low, E. Santelli, J. Pascual

Date :   11 Apr 09 (Deposition) - 16 Jun 09 (Release) - 18 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Bacteria Tir Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Chan, L. Y. Low, S. Hsu, S. Li, T. Liu, E. Santelli, G. Le Negrate, J. C. Reed, V. L. Woods, J. Pascual
Molecular Mimicry In Innate Immunity: Crystal Structure Of A Bacterial Tir Domain.
J. Biol. Chem. V. 284 21386 2009
PubMed-ID: 19535337 | Reference-DOI: 10.1074/JBC.C109.007591
(for further references see the PDB file header)

Molecule 1 - TIR PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	ROSETTA PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 146-299
	Gene	:	PDEN_0113, PDTLP
	Organism Scientific	:	PARACOCCUS DENITRIFICANS PD1222
	Organism Taxid	:	318586

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:177 , HIS C:186 , ARG C:189	BINDING SITE FOR RESIDUE SO4 C 1

(no "SS Bond" information available for 3H16)

(no "Cis Peptide Bond" information available for 3H16)

(no "SAP(SNP)/Variant" information available for 3H16)

(no "PROSITE Motif" information available for 3H16)

(no "Exon" information available for 3H16)

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:136
 aligned with A1AY86_PARDP | A1AY86 from UniProtKB/TrEMBL  Length:299

    Alignment length:136
                                   172       182       192       202       212       222       232       242       252       262       272       282       292      
         A1AY86_PARDP   163 APPHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIR 298
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh..hhhhhhhhhhhh...eehhh.ee....hhhhhhhhhhh.eeeeeeeeehhhhh...hhhhhhhhh.........eeeeee...hhhhh...........ee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h16 A 163 APPHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIR 298
                                   172       182       192       202       212       222       232       242       252       262       272       282       292

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with A1AY86_PARDP | A1AY86 from UniProtKB/TrEMBL  Length:299

    Alignment length:137
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       
         A1AY86_PARDP   163 APPHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIRD 299
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh.hhhhhhhhhhhhh...eehhh.ee....hhhhhhhhhhhheeeeeeeehhhhhh...hhhhhhhhhh........eeeee...hhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h16 B 163 APPHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIRD 299
                                   172       182       192       202       212       222       232       242       252       262       272       282       292

Chain C from PDB  Type:PROTEIN  Length:127
 aligned with A1AY86_PARDP | A1AY86 from UniProtKB/TrEMBL  Length:299

    Alignment length:134
                                   174       184       194       204       214       224       234       244       254       264       274       284       294    
         A1AY86_PARDP   165 PHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIR 298
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhh..hhhhhhhhhhhh...eehhh.ee....hhhhhhhhhhh...eeeeeeehhhhh...hhhhhhh..-------..eeeeee..hhhhhhh.hhhhhhh..ee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h16 C 165 PHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLF-------SRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIR 298
                                   174       184       194       204       214       224       234       244       254       264       274       284       294    
                                                                                                         244     252

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with A1AY86_PARDP | A1AY86 from UniProtKB/TrEMBL  Length:299

    Alignment length:135
                                   173       183       193       203       213       223       233       243       253       263       273       283       293     
         A1AY86_PARDP   164 PPHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIR 298
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhh.hhhhhhhhhhhh....eehhh.ee....hhhhhhhhhhh.eeeeeeeehhhhhh...hhhhhhhhhh-----...eeeee...hhhhhhh..........ee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h16 D 164 PPHDIFISHAWEDKADFVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIVVLSTHFFKKEWPQKELDGLFQ-----RSRILPIWHKVSKDEVASFSPTMADKLAFNTSTKSVDEIVADLMAIIR 298
                                   173       183       193       203       213       223       233       243 |     253       263       273       283       293     
                                                                                                           245   251

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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 '\|'

(no "SCOP Domain" information available for 3H16)

(no "CATH Domain" information available for 3H16)

(no "Pfam Domain" information available for 3H16)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (A1AY86_PARDP | A1AY86)

biological process
	GO:0007165		signal transduction		The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

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