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Title :   CRYSTAL STRUCTURE OF MANNOBIOSE BOUND OLIGOPEPTIDE ABC TRANSPORTER, PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN (TM1223) FROM THERMOTOGA MARITIMA AT 1.75 A RESOLUTION

Authors :   X. Lu, S. Ghimire-Rijal, M. J. Cuneo

Date :   30 Apr 14 (Deposition) - 17 Sep 14 (Release) - 05 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ghimire-Rijal, X. Lu, D. A. Myles, M. J. Cuneo
Duplication Of Genes In An Atp-Binding Cassette Transport System Increases Dynamic Range While Maintaining Ligand Specificity.
J. Biol. Chem. V. 289 30090 2014
PubMed-ID: 25210043 | Reference-DOI: 10.1074/JBC.M114.590992

Molecule 1 - ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM_1223, THEMA_08215, TMARI_1230
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
	Synonym	:	MANNOSIDE ABC TRANSPORT SYSTEM,SUGAR-BINDING PROTEIN, OLIGOPEPTIDE ABC TRANSPORTER,PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	MAB	2	Ligand/Ion	MANNOBIOSE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	NO3	3	Ligand/Ion	NITRATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MAB	1	Ligand/Ion	MANNOBIOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MAB	1	Ligand/Ion	MANNOBIOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NO3	2	Ligand/Ion	NITRATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:32 , ALA A:33 , TRP A:35 , ASN A:231 , ASN A:247 , PHE A:248 , PHE A:249 , TRP A:387 , ASP A:389 , TRP A:390 , ASN A:433 , PHE A:434 , ASN A:512 , TRP A:515 , TRP A:539 , HOH A:846 , HOH A:848 , HOH A:867 , HOH A:885 , HOH A:910 , HOH A:923	binding site for residue MAB A 601
2	AC2	SOFTWARE	ASP A:362 , ASN A:364 , ASP A:366 , PHE A:368 , GLU A:370 , HOH A:1262	binding site for residue MG A 602
3	AC3	SOFTWARE	ARG A:227 , VAL A:228 , LEU A:229 , VAL A:233 , HOH A:1328 , VAL B:228 , LEU B:229	binding site for residue NO3 A 603
4	AC4	SOFTWARE	GLY B:32 , ALA B:33 , ASN B:231 , ASN B:247 , PHE B:248 , PHE B:249 , TRP B:387 , ASP B:389 , TRP B:390 , ASN B:433 , PHE B:434 , ASN B:512 , TRP B:515 , TRP B:539 , HOH B:860 , HOH B:866 , HOH B:872 , HOH B:879 , HOH B:941 , HOH B:998	binding site for residue MAB B 601
5	AC5	SOFTWARE	ASP B:362 , ASN B:364 , ASP B:366 , PHE B:368 , GLU B:370	binding site for residue MG B 602
6	AC6	SOFTWARE	ARG B:96 , TRP B:97 , GLN B:98 , GLY B:100 , ASN B:205 , ASN B:207 , HOH B:788 , HOH B:1038	binding site for residue NO3 B 603
7	AC7	SOFTWARE	TYR B:191 , HOH B:943	binding site for residue NO3 B 604

(no "SS Bond" information available for 4PFT)

Asymmetric Unit

No.	Residues
1	Ala A:269	-	Pro A:270
2	Tyr A:287	-	Pro A:288
3	Ala B:269	-	Pro B:270
4	Tyr B:287	-	Pro B:288

(no "SAP(SNP)/Variant" information available for 4PFT)

(no "PROSITE Motif" information available for 4PFT)

(no "Exon" information available for 4PFT)

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:537
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeee..............................eeee....eeee..eeeeee....eeeeee............hhhhhhhhhhhhhhh....hhhhhh.eeeeeeee..eeeeee...hhhhhhhhhhhh...hhhhhh..hhhhhhhh..........eeeeeee..eeeeee...hhhhhhhh......eeeee...hhhhhhhhhhh....ee.....hhhhhhhhhh............eeeeeeeee........hhhhhhhhhhhhhhhhhhhhh...............hhhhhh..hhhhhhhhh...hhhhhhhhhhhhh...................eeee....hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeeeee...ee....ee.................hhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pft A  22 FERNKTLYWGGALWSPPSNWNPFTPWNAVAGTIGLVYEPLFLYDPLNDKFEPWLAEKGEWVSNNEYVLTLRKGLRWQDGVPLTADDVVFTFEIAKKYTGISYSPVWNWLGRIERVDERTLKFVFSDPRYQEWKQMLINTPIVPKHIWENKTEEEVLQAANENPVGSGPYYVESWADDRCVFKKNGNWWGIRELGYDPKPERIVELRVLSNNVAVGMLMKGELDWSNFFLPGVPVLKKAYGIVTWYENAPYMLPANTAGIYINVNKYPLSIPEFRRAMAYAINPEKIVTRAYENMVTAANPAGILPLPGYMKYYPKEVVDKYGFKYDPEMAKKILDELGFKDVNKDGFREDPNGKPFKLTIECPYGWTDWMVSIQSIAEDLVKVGINVEPKYPDYSKYADDLYGGKFDLILNNFTTGVSATIWSYFNGVFYPDAVESEYSYSGNFGKYANPEVETLLDELNRSNDDAKIKEVVAKLSEILLKDLPFIPLWYNGAWFQASEAVWTNWPTEKNPYAVPIGWNGWWQLTGIKTLFGIEAKH 558
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551

Chain B from PDB  Type:PROTEIN  Length:538
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeee..............................eeee....eeee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhh....hhhhhh.eeeeeeee..eeeeee...hhhhhhhhhhhh...hhhhhh..hhhhhhhh..........eeeeeee..eeeeee...hhhhhhh.......eeeee...hhhhhhhhhhh....ee.....hhhhhhhhhh............eeeeeeeee........hhhhhhhhhhhhhhhhhhhhh...............hhhhhh..hhhhhhhhh...hhhhhhhhhhhhh...................eeee....hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeeee...ee....ee.................hhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pft B  21 TFERNKTLYWGGALWSPPSNWNPFTPWNAVAGTIGLVYEPLFLYDPLNDKFEPWLAEKGEWVSNNEYVLTLRKGLRWQDGVPLTADDVVFTFEIAKKYTGISYSPVWNWLGRIERVDERTLKFVFSDPRYQEWKQMLINTPIVPKHIWENKTEEEVLQAANENPVGSGPYYVESWADDRCVFKKNGNWWGIRELGYDPKPERIVELRVLSNNVAVGMLMKGELDWSNFFLPGVPVLKKAYGIVTWYENAPYMLPANTAGIYINVNKYPLSIPEFRRAMAYAINPEKIVTRAYENMVTAANPAGILPLPGYMKYYPKEVVDKYGFKYDPEMAKKILDELGFKDVNKDGFREDPNGKPFKLTIECPYGWTDWMVSIQSIAEDLVKVGINVEPKYPDYSKYADDLYGGKFDLILNNFTTGVSATIWSYFNGVFYPDAVESEYSYSGNFGKYANPEVETLLDELNRSNDDAKIKEVVAKLSEILLKDLPFIPLWYNGAWFQASEAVWTNWPTEKNPYAVPIGWNGWWQLTGIKTLFGIEAKH 558
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 4PFT)

(no "CATH Domain" information available for 4PFT)

(no "Pfam Domain" information available for 4PFT)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
		Ala A:269 - Pro A:270	[ RasMol ]
		Ala B:269 - Pro B:270	[ RasMol ]
		Tyr A:287 - Pro A:288	[ RasMol ]
		Tyr B:287 - Pro B:288	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

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