1NC9 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   STREPTAVIDIN MUTANT Y43A WITH IMINOBIOTIN AT 1.8A RESOLUTION

Authors :   I. Le Trong, S. Freitag, L. A. Klumb, V. Chu, P. S. Stayton, R. E. Stenkamp

Date :   05 Dec 02 (Deposition) - 02 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Tetramer, Biotin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Le Trong, S. Freitag, L. A. Klumb, V. Chu, P. S. Stayton, R. E. Stenkamp
Structural Studies Of Hydrogen Bonds In The High-Affinity Streptavidin-Biotin Complex: Mutations Of Amino Acids Interacting With The Ureido Oxygen Of Biotin.
Acta Crystallogr. , Sect. D V. 59 1567 2003
PubMed-ID: 12925786 | Reference-DOI: 10.1107/S0907444903014562
(for further references see the PDB file header)

Molecule 1 - STREPTAVIDIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE STREPAVIDIN, RESIDUES 13-139
	Gene	:	CORE STREPTAVIDIN
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	IMI	1	Ligand/Ion	2-IMINOBIOTIN

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:23 , SER A:27 , SER A:45 , VAL A:47 , GLY A:48 , ASN A:49 , TRP A:79 , SER A:88 , THR A:90 , TRP A:108 , ASP A:128 , TRP D:120	BINDING SITE FOR RESIDUE IMI A 5100

(no "SS Bond" information available for 1NC9)

(no "Cis Peptide Bond" information available for 1NC9)

(no "SAP(SNP)/Variant" information available for 1NC9)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	A:118-132 B:118-132 C:118-132 D:118-132

(no "Exon" information available for 1NC9)

Asymmetric/Biological 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:120
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:120
                                    49        59        69        79        89        99       109       119       129       139       149       159
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d1nc9a_ A: Streptavidin                                                                                                  SCOP domains
               CATH domains 1nc9A00 A:16-135  [code=2.40.128.30, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nc9 A  16 GITGTWYNQLGSTFIVTAGADGALTGTAESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    25        35        45        55        65        75        85        95       105       115       125       135

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1nc9b_ B: Streptavidin                                                                                                SCOP domains
               CATH domains 1nc9B00 B:16-133  [code=2.40.    128.30, no name defined]                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee----hhhhheeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc9 B  16 GITGTWYNQLGSTFIVTAGADGALTGTAE----NAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        |-   |    55        65        75        85        95       105       115       125        
                                                       44   49

Chain C from PDB  Type:PROTEIN  Length:111
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1nc9c_ C: Streptavidin                                                                                                SCOP domains
               CATH domains 1nc9C00 C:16-133  [code=2.40.       128.30, no name defined]                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee-------..eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc9 C  16 GITGTWYNQLGSTFIVTAGADGALTGTAE-------SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        |-      | 55        65        75        85        95       105       115       125        
                                                       44      52

Chain D from PDB  Type:PROTEIN  Length:111
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1nc9d_ D: Streptavidin                                                                                                SCOP domains
               CATH domains 1nc9D00 D:16-133  [code=2.40.       128.30, no name defined]                                                           CATH domains
           Pfam domains (1) Avidin-1nc9D01 D:16-132                                                                                              - Pfam domains (1)
           Pfam domains (2) Avidin-1nc9D02 D:16-132                                                                                              - Pfam domains (2)
           Pfam domains (3) Avidin-1nc9D03 D:16-132                                                                                              - Pfam domains (3)
           Pfam domains (4) Avidin-1nc9D04 D:16-132                                                                                              - Pfam domains (4)
         Sec.struct. author ...eeeee....eeeeee....eeeeeee-------..eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1nc9 D  16 GITGTWYNQLGSTFIVTAGADGALTGTAE-------SRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        |-      | 55        65        75        85        95       105       115       125        
                                                       44      52

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Streptavidin-like (225)

Superfamily: Avidin/streptavidin (197)

Family: Avidin/streptavidin (181)

Protein domain: Streptavidin (121)

Streptomyces avidinii [TaxId: 1895] (121)

1a	d1nc9a_	A:
1b	d1nc9b_	B:
1c	d1nc9c_	C:
1d	d1nc9d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.30, no name defined] (148)

Streptomyces avidinii. Organism_taxid: 1895. (29)

1a	1nc9A00	A:16-135
1b	1nc9B00	B:16-133
1c	1nc9C00	C:16-133
1d	1nc9D00	D:16-133

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Avidin] (113)

Family: Avidin (113)

Streptomyces avidinii (97)

1a	Avidin-1nc9D01	D:16-132
1b	Avidin-1nc9D02	D:16-132
1c	Avidin-1nc9D03	D:16-132
1d	Avidin-1nc9D04	D:16-132

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (SAV_STRAV | P22629)

cellular component
	GO:0005576		extracellular region		The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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1n43	STREPTAVIDIN MUTANT N23A WITH BIOTIN AT 1.89A RESOLUTION
1n4j	STREPTAVIDIN MUTANT N23A AT 2.18A RESOLUTION
1n7y	STREPTAVIDIN MUTANT N23E AT 1.96A RESOLUTION
1n9m	STREPTAVIDIN MUTANT S27A WITH BIOTIN AT 1.6A RESOLUTION
1n9y	STREPTAVIDIN MUTANT S27A AT 1.5A RESOLUTION
1nbx	STREPTAVIDIN MUTANT Y43A AT 1.70A RESOLUTION

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Ligands, Modified Residues, Ions (1, 1)

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