4JAW - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LACTO-N-BIOSIDASE FROM BIFIDOBACTERIUM BIFIDUM COMPLEXED WITH LNB-THIAZOLINE

Authors :   T. Ito, T. Katayama, K. A. Stubbs, S. Fushinobu

Date :   19 Feb 13 (Deposition) - 20 Mar 13 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Alpha/Beta-Domain, Tim Barrel, Beta-Trefoil, Hydrolase, Membrane- Anchored Extracellular (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ito, T. Katayama, M. Hattie, H. Sakurama, J. Wada, R. Suzuki, H. Ashida, T. Wakagi, K. Yamamoto, K. A. Stubbs, S. Fushinobu
Crystal Structures Of A Glycoside Hydrolase Family 20 Lacto-N-Biosidase From Bifidobacterium Bifidum
J. Biol. Chem. V. 288 11795 2013
PubMed-ID: 23479733 | Reference-DOI: 10.1074/JBC.M112.420109
(for further references see the PDB file header)

Molecule 1 - LACTO-N-BIOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.140
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28B
	Expression System Strain	:	BL21(DE3) CODONPLUS-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUE 41-663
	Gene	:	LNBB
	Organism Scientific	:	BIFIDOBACTERIUM BIFIDUM
	Organism Taxid	:	398514
	Strain	:	JCM1254

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	NGT	2	Ligand/Ion	3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NGT	1	Ligand/Ion	3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NGT	1	Ligand/Ion	3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 11)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	NGT	2	Ligand/Ion	3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
3	SO4	7	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:190 , GLU A:216 , ASN A:259 , HIS A:263 , ASP A:320 , PRO A:466 , ASP A:467 , NGT A:702 , HOH A:832 , HOH A:981	BINDING SITE FOR RESIDUE GAL A 701
02	AC2	SOFTWARE	ASP A:320 , GLU A:321 , TRP A:373 , TYR A:419 , TYR A:427 , TRP A:465 , ASP A:467 , GAL A:701	BINDING SITE FOR RESIDUE NGT A 702
03	AC3	SOFTWARE	SER A:423 , ALA A:424 , GLN A:425 , VAL A:426 , PHE A:471 , ARG A:599 , HOH A:950	BINDING SITE FOR RESIDUE SO4 A 703
04	AC4	SOFTWARE	THR A:146 , ASP A:147 , HOH A:927 , HOH A:928	BINDING SITE FOR RESIDUE SO4 A 704
05	AC5	SOFTWARE	TYR A:395 , ARG A:587	BINDING SITE FOR RESIDUE SO4 A 705
06	AC6	SOFTWARE	GLN A:190 , ASN A:265 , ASN A:286 , HOH A:842 , HOH A:932	BINDING SITE FOR RESIDUE SO4 A 706
07	AC7	SOFTWARE	GLN B:190 , GLU B:216 , ASN B:259 , HIS B:263 , ASP B:320 , PRO B:466 , ASP B:467 , NGT B:702 , HOH B:893 , HOH B:960	BINDING SITE FOR RESIDUE GAL B 701
08	AC8	SOFTWARE	ASP B:320 , GLU B:321 , TRP B:373 , TRP B:394 , TYR B:419 , TYR B:427 , TRP B:465 , ASP B:467 , GAL B:701	BINDING SITE FOR RESIDUE NGT B 702
09	AC9	SOFTWARE	SER B:423 , ALA B:424 , GLN B:425 , VAL B:426 , PHE B:471 , ARG B:599 , HOH B:939 , HOH B:945	BINDING SITE FOR RESIDUE SO4 B 703
10	BC1	SOFTWARE	TYR B:395 , ARG B:587	BINDING SITE FOR RESIDUE SO4 B 704
11	BC2	SOFTWARE	GLN B:190 , ASN B:265 , ASN B:286 , HOH B:899 , HOH B:900	BINDING SITE FOR RESIDUE SO4 B 705

Asymmetric Unit

No.	Residues
1	A:187	-	A:189
2	A:564	-	A:589
3	B:187	-	B:189
4	B:564	-	B:589

Asymmetric Unit

No.	Residues
1	Val A:56	-	Pro A:57
2	Trp A:232	-	Ser A:233
3	Ser A:260	-	Pro A:261
4	Gly A:542	-	Pro A:543
5	Lys A:616	-	Asp A:617
6	Val B:56	-	Pro B:57
7	Gly B:107	-	Ser B:108
8	Trp B:232	-	Ser B:233
9	Ser B:260	-	Pro B:261
10	Gly B:542	-	Pro B:543

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

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

(no "Exon" information available for 4JAW)

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:633
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....eee...................eeeeeeee.....eee....hhhhhhhhhhhhhhhhh...eee........eeeee...hhhhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhhh...eeeee.........hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhh.hhh.eee.....eeeeee...hhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeee.hhh............eeee......hhhhhhhhh..eee.hhh.eee........hhhhhhhh.....ee...ee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhh.......eeeehhhhh......eeeee.....eeeee.....eee.....ee..ee.......eee..........hhhhhhhhhh..eeeee.....eeeee.....eeee......hhhhhhh......eeeehhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jaw A  30 SSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQRLAIATGNEQNIDLETHRPAAGTVAQFPADLVS 662
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659

Chain B from PDB  Type:PROTEIN  Length:632
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....eee...................eeeeeeee.....eeee...hhhhhhhhhhhhhhhhh...eeee.......eeeee...hhhhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhhh...eeeee.........hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhh.hhh.eee.....eeeeee...hhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeee.hhh............eeee......hhhhhhhhh..eee.hhh.eee........hhhhhhhh.....ee...ee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhh........eeeehhhhh......eeeee.....eeeee.....eee.....ee..ee.......eee..........hhhhhhhhhh..eeeee.....eeeee.....eeee......hhhhhhh......eeeehhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jaw B  30 SSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQRLAIATGNEQNIDLETHRPAAGTVAQFPADLV 661
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659

Legend:		→ Mismatch	(orange background)
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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 4JAW)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:542 - Pro A:543	[ RasMol ]
		Gly B:107 - Ser B:108	[ RasMol ]
		Gly B:542 - Pro B:543	[ RasMol ]
		Lys A:616 - Asp A:617	[ RasMol ]
		Ser A:260 - Pro A:261	[ RasMol ]
		Ser B:260 - Pro B:261	[ RasMol ]
		Trp A:232 - Ser A:233	[ RasMol ]
		Trp B:232 - Ser B:233	[ RasMol ]
		Val A:56 - Pro A:57	[ RasMol ]
		Val B:56 - Pro B:57	[ RasMol ]

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	B3TLD6_BIFBI \| B3TLD6	:	4h04 5bxp 5bxr 5bxs 5bxt

4h04	THE SAME PROTEIN COMPLEXED WITH LACTO-N-BIOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (4, 4)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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