2FN9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THERMOTOGA MARITIMA RIBOSE BINDING PROTEIN UNLIGANDED FORM

Authors :   M. J. Cuneo, A. Changela, Y Tian, L. S. Beese, H. W. Hellinga

Date :   10 Jan 06 (Deposition) - 16 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Rbp, Ribose Binding Protein, Periplasmic Binding Protein, Thermophilic Proteins, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Cuneo, L. S. Beese, H. W. Hellinga
Ligand-Induced Conformational Changes In A Thermophilic Ribose-Binding Protein.
Bmc Struct. Biol. V. 8 50 2008
PubMed-ID: 19019243 | Reference-DOI: 10.1186/1472-6807-8-50

Molecule 1 - RIBOSE ABC TRANSPORTER, PERIPLASMIC RIBOSE-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21-ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0958
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2FN9)

(no "Site" information available for 2FN9)

(no "SS Bond" information available for 2FN9)

(no "Cis Peptide Bond" information available for 2FN9)

(no "SAP(SNP)/Variant" information available for 2FN9)

(no "PROSITE Motif" information available for 2FN9)

(no "Exon" information available for 2FN9)

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:280
 aligned with Q9X053_THEMA | Q9X053 from UniProtKB/TrEMBL  Length:323

    Alignment length:280
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
         Q9X053_THEMA    31 GKMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRGINARGLAVAQIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGRTDIYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIVPVTVELVTRE 310
               SCOP domains d2fn9a_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh...eeee...........eeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh.....eee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.......eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fn9 A   2 GKMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRGINARGLAVAQIYSDNYYGGVLAGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGRTDIYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIVPVTVELVTRE 281
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q9X053_THEMA | Q9X053 from UniProtKB/TrEMBL  Length:323

    Alignment length:280
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
         Q9X053_THEMA    31 GKMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRGINARGLAVAQIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGRTDIYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIVPVTVELVTRE 310
               SCOP domains d2fn9b_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh...eeee...........eeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh....eee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.......eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fn9 B   2 GKMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRGINARGLAVAQIYSDNYYGGVLAGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGRTDIYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIVPVTVELVTRE 281
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

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) (23833)

Fold: Periplasmic binding protein-like I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: automated matches (65)

Protein domain: automated matches (65)

Thermotoga maritima [TaxId: 243274] (4)

1a	d2fn9a_	A:
1b	d2fn9b_	B:

(no "CATH Domain" information available for 2FN9)

(no "Pfam Domain" information available for 2FN9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9X053_THEMA | Q9X053)

molecular function
	GO:0015145	monosaccharide transmembrane transporter activity	Enables the transfer of a monosaccharide from one side of a membrane to the other.
biological process
	GO:0015749	monosaccharide transport	The directed movement of monosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2fn9)

	Sites
(no "Sites" information available for 2fn9)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fn9)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2fn9
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		Orientation in Membranes	:	OPM
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	Q9X053_THEMA \| Q9X053
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UniProtKB/TrEMBL
	Q9X053_THEMA \| Q9X053	:	2fn8

2fn8	THERMOTOGA MARITIMA RIBOSE BINDING PROTEIN RIBOSE BOUND FORM
2fnc	THERMOTOGA MARITIMA MALTOTRIOSE BINDING PROTEIN BOUND WITH MALTOTRIOSE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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