1URP - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI

Authors :   A. J. Bjorkman, S. L. Mowbray

Date :   03 Apr 98 (Deposition) - 17 Jun 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Transport, Chemotaxis, Periplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Bjorkman, S. L. Mowbray
Multiple Open Forms Of Ribose-Binding Protein Trace The Path Of Its Conformational Change.
J. Mol. Biol. V. 279 651 1998
PubMed-ID: 9641984 | Reference-DOI: 10.1006/JMBI.1998.1785
(for further references see the PDB file header)

Molecule 1 - D-RIBOSE-BINDING PROTEIN
	Cellular Location	:	PERIPLASM
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	PERIPLASM
	Expression System Gene	:	RBSB
	Expression System Plasmid	:	PCMB1
	Expression System Strain	:	MRI7
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1URP)

(no "Site" information available for 1URP)

(no "SS Bond" information available for 1URP)

(no "Cis Peptide Bond" information available for 1URP)

(no "SAP(SNP)/Variant" information available for 1URP)

(no "PROSITE Motif" information available for 1URP)

(no "Exon" information available for 1URP)

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
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Chain A from PDB  Type:PROTEIN  Length:271
 aligned with RBSB_ECOLI | P02925 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:271
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           RBSB_ECOLI    26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 296
               SCOP domains d1urpa_ A: D-ribose-binding protein                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1urpA01 A:1-101,A:238-261  [code=3.40.50.2300, no name defined]                                      1urpA02 A:102-237,A:262-271  [code=3.40.50.2300, no name defined]                                                                       1urpA01                 1urpA02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhhhh..eeeee..........eee...hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh.....eee.....hhhhhhhh......eee..hhhhhhhhhhhhhhhh.............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urp A   1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with RBSB_ECOLI | P02925 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:271
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           RBSB_ECOLI    26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 296
               SCOP domains d1urpb_ B: D-ribose-binding protein                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1urpB01 B:1-101,B:238-261  [code=3.40.50.2300, no name defined]                                      1urpB02 B:102-237,B:262-271  [code=3.40.50.2300, no name defined]                                                                       1urpB01                 1urpB02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhhhh..eeeee..........eee...hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh.....eee.....hhhhhhhh......eee..hhhhhhhhhhhhhhhhh............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urp B   1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain C from PDB  Type:PROTEIN  Length:271
 aligned with RBSB_ECOLI | P02925 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:271
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           RBSB_ECOLI    26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 296
               SCOP domains d1urpc_ C: D-ribose-binding protein                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1urpC01 C:1-101,C:238-261  [code=3.40.50.2300, no name defined]                                      1urpC02 C:102-237,C:262-271  [code=3.40.50.2300, no name defined]                                                                       1urpC01                 1urpC02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhhhh..eeeee..........eee...hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh.....eee.....hhhhhhhh......eee..hhhhhhhhhhhhhhhhh............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urp C   1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain D from PDB  Type:PROTEIN  Length:271
 aligned with RBSB_ECOLI | P02925 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:271
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           RBSB_ECOLI    26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 296
               SCOP domains d1urpd_ D: D-ribose-binding protein                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1urpD01 D:1-101,D:238-261  [code=3.40.50.2300, no name defined]                                      1urpD02 D:102-237,D:262-271  [code=3.40.50.2300, no name defined]                                                                       1urpD01                 1urpD02    CATH domains
           Pfam domains (1) ---Peripla_BP_4-1urpD01 D:4-256                                                                                                                                                                                                                                 --------------- Pfam domains (1)
           Pfam domains (2) ---Peripla_BP_4-1urpD02 D:4-256                                                                                                                                                                                                                                 --------------- Pfam domains (2)
           Pfam domains (3) ---Peripla_BP_4-1urpD03 D:4-256                                                                                                                                                                                                                                 --------------- Pfam domains (3)
           Pfam domains (4) ---Peripla_BP_4-1urpD04 D:4-256                                                                                                                                                                                                                                 --------------- Pfam domains (4)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhhhh..eeeee..........eee...hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh.....eee.....hhhhhhhh......eee..hhhhhhhhhhhhhhhhh............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urp D   1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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: L-arabinose binding protein-like (114)

Protein domain: D-ribose-binding protein (6)

Escherichia coli, strain k-12 [TaxId: 562] (6)

1a	d1urpa_	A:
1b	d1urpb_	B:
1c	d1urpc_	C:
1d	d1urpd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. (3)

1a	1urpA02	A:102-237,A:262-271
1b	1urpC01	C:1-101,C:238-261
1c	1urpD01	D:1-101,D:238-261
1d	1urpB02	B:102-237,B:262-271
1e	1urpC02	C:102-237,C:262-271
1f	1urpD02	D:102-237,D:262-271
1g	1urpA01	A:1-101,A:238-261
1h	1urpB01	B:1-101,B:238-261

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: Peripla_BP_4 (17)

Escherichia coli (strain K12) (7)

1a	Peripla_BP_4-1urpD01	D:4-256
1b	Peripla_BP_4-1urpD02	D:4-256
1c	Peripla_BP_4-1urpD03	D:4-256
1d	Peripla_BP_4-1urpD04	D:4-256

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RBSB_ECOLI | P02925)

molecular function
	GO:0015145	monosaccharide transmembrane transporter activity	Enables the transfer of a monosaccharide from one side of a membrane to the other.
	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:0008643	carbohydrate transport	The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	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.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
	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.

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