1VKF - JenaLib

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Title :   CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   13 May 04 (Deposition) - 25 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Glycerol Uptake Operon Antiterminator-Related Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Glycerol Uptake Operon Antiterminator-Related Protein (Tm1436) From Thermotoga Maritima At 1. 65 A Resolution
To Be Published
PubMed: search

Molecule 1 - GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM1436
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	CIT	3	Ligand/Ion	CITRIC ACID
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:101 , SER A:102 , TRP B:10 , GLY B:144 , LEU B:145 , THR B:164 , SER B:165 , HOH B:402 , HOH B:425	BINDING SITE FOR RESIDUE PO4 B 401
2	AC2	SOFTWARE	TRP A:10 , LEU A:26 , ARG A:96 , ALA A:143 , GLY A:144 , LEU A:145 , SER A:163 , THR A:164 , SER A:165 , HOH A:518 , HOH A:538 , HOH A:589 , ASP B:101 , SER B:102	BINDING SITE FOR RESIDUE CIT A 501
3	AC3	SOFTWARE	TRP C:10 , LEU C:26 , ASP C:101 , SER C:102 , LEU C:123 , GLY C:144 , LEU C:145 , SER C:163 , THR C:164 , SER C:165 , HOH C:529 , HOH C:572	BINDING SITE FOR RESIDUE CIT C 502
4	AC4	SOFTWARE	ALA D:8 , TRP D:10 , LEU D:26 , SER D:102 , ALA D:143 , GLY D:144 , LEU D:145 , SER D:163 , THR D:164 , SER D:165 , HOH D:535	BINDING SITE FOR RESIDUE CIT D 503

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

Asymmetric Unit

No.	Residues
1	Leu A:123	-	Pro A:124
2	Leu B:123	-	Pro B:124
3	Mse B:172	-	Lys B:173
4	Leu C:123	-	Pro C:124
5	Leu D:123	-	Pro D:124

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

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

(no "Exon" information available for 1VKF)

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:172
 aligned with Q9X1F0_THEMA | Q9X1F0 from UniProtKB/TrEMBL  Length:176

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q9X1F0_THEMA     1 MFKGIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKM 172
               SCOP domains d1vkfa_ A: Glycerol uptake operon antiterminator-related protein TM1436                                                                                                      SCOP domains
               CATH domains -1vkfA00 A:2-171 GlpP-like                                                                                                                                                 - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee............eeee..ee..hhhhhhhhhhhh..eeeee...ee....hhhhhhhhhhhh..eeee.hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeeee....hhhhhhhhh....eeee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkf A   1 mFKGIIAALWDmDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDmDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKm 172
                            |       10 |      20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170 |
                            |         12-MSE                                 51-MSE                                                                                                                  172-MSE
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q9X1F0_THEMA | Q9X1F0 from UniProtKB/TrEMBL  Length:176

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         Q9X1F0_THEMA     1 MFKGIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKMK 173
               SCOP domains d1vkfb_ B: Glycerol uptake operon antiterminator-related protein TM1436                                                                                                       SCOP domains
               CATH domains -1vkfB00 B:2-173 GlpP-like                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee............eeee..ee..hhhhhhhhhhh...eeeee...ee....hhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeeee....hhhhhhhhhh...eeee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkf B   1 mFKGIIAALWDmDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDmDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKmK 173
                            |       10 |      20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170 | 
                            |         12-MSE                                 51-MSE                                                                                                                  172-MSE
                            1-MSE

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with Q9X1F0_THEMA | Q9X1F0 from UniProtKB/TrEMBL  Length:176

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         Q9X1F0_THEMA     1 MFKGIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKMK 173
               SCOP domains d1vkfc_ C: Glycerol uptake operon antiterminator-related protein TM1436                                                                                                       SCOP domains
               CATH domains -1vkfC00 C:2-173 GlpP-like                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee............eeee..ee..hhhhhhhhhhhh..eeeee...ee....hhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh...eeeee....hhhhhhhhh....eeee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkf C   1 mFKGIIAALWDmDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDmDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKmK 173
                            |       10 |      20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170 | 
                            |         12-MSE                                 51-MSE                                                                                                                  172-MSE
                            1-MSE

Chain D from PDB  Type:PROTEIN  Length:172
 aligned with Q9X1F0_THEMA | Q9X1F0 from UniProtKB/TrEMBL  Length:176

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q9X1F0_THEMA     1 MFKGIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKM 172
               SCOP domains d1vkfd_ D: Glycerol uptake operon antiterminator-related protein TM1436                                                                                                      SCOP domains
               CATH domains -1vkfD00 D:2-171 GlpP-like                                                                                                                                                 - CATH domains
           Pfam domains (1) G3P_antiterm-1vkfD01 D:1-171                                                                                                                                               - Pfam domains (1)
           Pfam domains (2) G3P_antiterm-1vkfD02 D:1-171                                                                                                                                               - Pfam domains (2)
           Pfam domains (3) G3P_antiterm-1vkfD03 D:1-171                                                                                                                                               - Pfam domains (3)
           Pfam domains (4) G3P_antiterm-1vkfD04 D:1-171                                                                                                                                               - Pfam domains (4)
         Sec.struct. author ...eeeeee....hhhhh...eeee..ee..hhhhhhhhhhhh..eeeee...ee....hhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh....eeeee....hhhhhhhhhhhh.eeee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkf D   1 mFKGIIAALWDmDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDmDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKm 172
                            |       10 |      20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170 |
                            |         12-MSE                                 51-MSE                                                                                                                  172-MSE
                            1-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: GlpP-like (1)

Family: GlpP-like (1)

Protein domain: Glycerol uptake operon antiterminator-related protein TM1436 (1)

Thermotoga maritima [TaxId: 2336] (1)

1a	d1vkfa_	A:
1b	d1vkfb_	B:
1c	d1vkfc_	C:
1d	d1vkfd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: GlpP-like (1)

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8. (1)

1a	1vkfA00	A:2-171
1b	1vkfB00	B:2-173
1c	1vkfC00	C:2-173
1d	1vkfD00	D:2-171

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: G3P_antiterm (1)

Thermotoga maritima (1)

1a	G3P_antiterm-1vkfD01	D:1-171
1b	G3P_antiterm-1vkfD02	D:1-171
1c	G3P_antiterm-1vkfD03	D:1-171
1d	G3P_antiterm-1vkfD04	D:1-171

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9X1F0_THEMA | Q9X1F0)

biological process
	GO:0006355		regulation of transcription, DNA-templated		Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009607		response to biotic stimulus		Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.

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