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Description

Title :   CRYSTAL STRUCTURE OF THE REFOLDED R7-2 STREPTAVIDIN

Authors :   V. N Malashkevich, M. Magalhaes, C. M. Czecster, R. Guan, M. Levy, S. C.

Date :   01 Apr 11 (Deposition) - 06 Jul 11 (Release) - 06 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (4x)

Keywords :   Streptavidin Variants, Improved Desthiobiotin Binding, Opened Loop Destabilization, Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Magalhaes, C. M. Czekster, R. Guan, V. N. Malashkevich, S. C. Almo M. Levy
Evolved Streptavidin Mutants Reveal Key Role Of Loop Residu In High-Affinity Binding.
Protein Sci. V. 20 1145 2011
PubMed-ID: 21520321 | Reference-DOI: 10.1002/PRO.642

Compounds

Molecule 1 - STREPTAVIDIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCR2.1-TOPO
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 37-164
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES AVIDINII
	Organism Taxid	:	1895

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	1PE	4	Ligand/Ion	PENTAETHYLENE GLYCOL

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:45 , VAL A:47 , GLY A:48 , ASN A:49 , TRP A:79 , SER A:88 , TRP A:120 , ASP A:128 , HOH A:267	BINDING SITE FOR RESIDUE 1PE A 700

SS Bonds (0, 0)

(no "SS Bond" information available for 3RDS)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3RDS)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3RDS)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	1	A:13-134
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	1	A:118-132

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	1	A:13-134
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	1	A:118-132

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AVIDIN_2	PS51326	Avidin-like domain profile.	SAV_STRAV	37-159	4	A:13-134
2	AVIDIN_1	PS00577	Avidin-like domain signature.	SAV_STRAV	142-156	4	A:118-132

Exons (0, 0)

(no "Exon" information available for 3RDS)

Sequences/Alignments

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:123
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:123
                                    45        55        65        75        85        95       105       115       125       135       145       155   
            SAV_STRAV    36 AAEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d3rdsa_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Avidin-3rdsA01 A:15-132                                                                                               -- Pfam domains
         Sec.struct. author hhhhhhheeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -AVIDIN_2  PDB: A:13-134 UniProt: 37-159                                                                                    PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rds A  12 TAEAGITGTWYNQLGSTLIVTAGADGALTGTYESAVGNAEGSYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSASTWSGQYVGGAEARINTQVLTTSGTTEANAWKSTLVGHDTFTKVK 134
                                    21        31        41        51        61        71        81        91       101       111       121       131

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric 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: automated matches (50)

Streptomyces avidinii [TaxId: 1895] (27)

d3rdsa_

CATH Domains (0, 0)

(no "CATH Domain" information available for 3RDS)

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Avidin (113)

Streptomyces avidinii (97)

Avidin-3rdsA01

A:15-132

Gene Ontology (1, 1)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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	Cis Peptide Bonds
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Biological Units
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	SAV_STRAV \| P22629	:	1df8 1hqq 1hxl 1hxz 1hy2 1i9h 1kff 1kl3 1kl4 1kl5 1lcv 1lcw 1lcz 1luq 1mep 1mk5 1mm9 1moy 1n43 1n4j 1n7y 1n9m 1n9y 1nbx 1nc9 1ndj 1nqm 1pts 1rst 1rsu 1rxh 1rxj 1rxk 1sld 1sle 1slf 1slg 1sre 1srf 1srg 1srh 1sri 1srj 1stp 1str 1sts 1swa 1swb 1swc 1swd 1swe 1swf 1swg 1swh 1swj 1swk 1swl 1swn 1swo 1swp 1swq 1swr 1sws 1swt 1swu 1vwa 1vwb 1vwc 1vwd 1vwe 1vwf 1vwg 1vwh 1vwi 1vwj 1vwk 1vwl 1vwm 1vwn 1vwo 1vwp 1vwq 1vwr 2bc3 2f01 2g5l 2gh7 2iza 2izb 2izc 2izd 2ize 2izf 2izg 2izh 2izi 2izj 2izk 2izl 2qcb 2rta 2rtb 2rtc 2rtd 2rte 2rtf 2rtg 2rth 2rti 2rtj 2rtk 2rtl 2rtm 2rtn 2rto 2rtp 2rtq 2rtr 2wpu 2y3e 2y3f 3mg5 3pk2 3rdm 3rdo 3rdq 3rdu 3rdx 3re5 3re6 3ry1 3ry2 3t6f 3t6l 3wyp 3wyq 3wzn 3wzo 3wzp 3wzq 3x00 4bx5 4bx6 4bx7 4cpe 4cpf 4cph 4cpi 4dne 4ekv 4gd9 4gda 4gjs 4gjv 4irw 4jo6 4oka 4y59 4y5d 4yvb 5b5f 5b5g 5cse 5f2b 5jd2 5k49 5k67 5k68 5l3y 5to2

Related Entries Specified in the PDB File

3rdm 3rdo 3rdq 3rdu 3rdx 3re5 3re6