1VQS - JenaLib

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Title :   CRYSTAL STRUCTURE OF A NIPSNAP FAMILY PROTEIN WITH UNKNOWN FUNCTION (ATU4242) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 1.50 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   20 Dec 04 (Deposition) - 11 Jan 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: C,D  (4x)
Biol. Unit 3: E  (5x)
Biol. Unit 4: E  (8x)

Keywords :   Ferredoxin-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Np_356412. 1) Fro Agrobacterium Tumefaciens At 1. 50 A Resolution
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN AGR_L_1239
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_356412.1
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS STR. C58
	Organism Taxid	:	176299
	Strain	:	C58 / ATCC 33970

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (4x)	:			C	D
Biological Unit 3 (5x)	:					E
Biological Unit 4 (8x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 27)

No.	Name	Count	Type	Full Name
1	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 44)

No.	Name	Count	Type	Full Name
1	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 44)

No.	Name	Count	Type	Full Name
1	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 25)

No.	Name	Count	Type	Full Name
1	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 40)

No.	Name	Count	Type	Full Name
1	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:9 , HOH B:298	BINDING SITE FOR RESIDUE SO4 B 105
2	AC2	SOFTWARE	ARG C:9	BINDING SITE FOR RESIDUE SO4 C 105
3	AC3	SOFTWARE	ARG D:9 , HOH D:288	BINDING SITE FOR RESIDUE SO4 D 105
4	AC4	SOFTWARE	ARG E:9 , HOH E:213 , HOH E:241	BINDING SITE FOR RESIDUE SO4 E 105
5	AC5	SOFTWARE	ARG A:9	BINDING SITE FOR RESIDUE SO4 A 105
6	AC6	SOFTWARE	GLY B:13 , ALA B:17 , HOH B:112 , HOH B:249 , HOH C:254	BINDING SITE FOR RESIDUE MPD B 106
7	AC7	SOFTWARE	PRO B:81 , HOH B:245 , GLY C:13 , ALA C:17 , ARG C:84 , HOH C:121 , HOH C:235	BINDING SITE FOR RESIDUE MPD C 106

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

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

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

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

(no "Exon" information available for 1VQS)

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:110
                                                                                                                                              
               SCOP domains d1vqsa_ A: Hypothetical protein Atu4242                                                                        SCOP domains
               CATH domains 1vqsA00 A:-5-103  [code=3.30.70.900, no name defined]                                                        - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1vqs A  -5 HHHHHHmFYEIRTYRLKNGAIPAYLKVVEDEGIEIQKSHLGELVGYFFSEIGPINEIVHIWAFSSLDDRAERRARLmADPRWLSFLPKIRDLIEVAENKImKPARFSPLm 104
                                  |  4        14        24        34        44        54        64      | 74        84        94|      104
                                  1-MSE                                                                71-MSE                  95-MSE  104-MSE

Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains d1vqsb_ B: Hypothetical protein Atu4242                                                                         SCOP domains
               CATH domains 1vqsB00 B:-6-103  [code=3.30.70.900, no name defined]                                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhheeeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1vqs B  -6 IHHHHHHmFYEIRTYRLKNGAIPAYLKVVEDEGIEIQKSHLGELVGYFFSEIGPINEIVHIWAFSSLDDRAERRARLmADPRWLSFLPKIRDLIEVAENKImKPARFSPLm 104
                                   | 3        13        23        33        43        53        63       |73        83        93 |     103|
                                   1-MSE                                                                71-MSE                  95-MSE  104-MSE

Chain C from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d1vqsc_ C: Hypothetical protein Atu4242                                                                        SCOP domains
               CATH domains 1vqsC00 C:-5-103  [code=3.30.70.900, no name defined]                                                        - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhheeeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1vqs C  -5 HHHHHHmFYEIRTYRLKNGAIPAYLKVVEDEGIEIQKSHLGELVGYFFSEIGPINEIVHIWAFSSLDDRAERRARLmADPRWLSFLPKIRDLIEVAENKImKPARFSPLm 104
                                  |  4        14        24        34        44        54        64      | 74        84        94|      104
                                  1-MSE                                                                71-MSE                  95-MSE  104-MSE

Chain D from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d1vqsd_ D: Hypothetical protein Atu4242                                                                        SCOP domains
               CATH domains 1vqsD00 D:-5-103  [code=3.30.70.900, no name defined]                                                        - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1vqs D  -5 HHHHHHmFYEIRTYRLKNGAIPAYLKVVEDEGIEIQKSHLGELVGYFFSEIGPINEIVHIWAFSSLDDRAERRARLmADPRWLSFLPKIRDLIEVAENKImKPARFSPLm 104
                                  |  4        14        24        34        44        54        64      | 74        84        94|      104
                                  1-MSE                                                                71-MSE                  95-MSE  104-MSE

Chain E from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d1vqse_ E: Hypothetical protein Atu4242                                                                        SCOP domains
               CATH domains 1vqsE00 E:-5-103  [code=3.30.70.900, no name defined]                                                        - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.eeeeee.......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1vqs E  -5 HHHHHHmFYEIRTYRLKNGAIPAYLKVVEDEGIEIQKSHLGELVGYFFSEIGPINEIVHIWAFSSLDDRAERRARLmADPRWLSFLPKIRDLIEVAENKImKPARFSPLm 104
                                  |  4        14        24        34        44        54        64      | 74        84        94|      104
                                  1-MSE                                                                71-MSE                  95-MSE  104-MSE

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Dimeric alpha+beta barrel (122)

Family: NIPSNAP (3)

Protein domain: Hypothetical protein Atu4242 (2)

Agrobacterium tumefaciens [TaxId: 358] (2)

1a	d1vqsa_	A:
1b	d1vqsb_	B:
1c	d1vqsc_	C:
1d	d1vqsd_	D:
1e	d1vqse_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.900, no name defined] (47)

C58 (Agrobacterium tumefaciens str) (4)

1a	1vqsA00	A:-5-103
1b	1vqsC00	C:-5-103
1c	1vqsD00	D:-5-103
1d	1vqsE00	E:-5-103
1e	1vqsB00	B:-6-103

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Description

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Ligands, Modified Residues, Ions (3, 27)

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