3OXN - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR FROM VIBRIO PARAHAEMOLYTICUS

Authors :   Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)

Date :   21 Sep 10 (Deposition) - 13 Oct 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Putative Transcriptional Regulator, Psi, Sgx, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of A Putative Transcriptional Regulator From Vibrio Parahaemolyticus
To Be Published
PubMed: search

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REGULATOR, LYSR FAMILY
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21 (DE3) CODON+RIL STRATAGENE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 99-330
	Gene	:	VP0027
	Organism Scientific	:	VIBRIO PARAHAEMOLYTICUS
	Organism Taxid	:	670

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 21)

No.	Name	Count	Type	Full Name
1	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 11)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH D:58 , THR D:123 , HIS D:154 , ARG D:172 , ILE D:220 , SER D:221 , TYR D:291	BINDING SITE FOR RESIDUE SO4 D 1

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

Asymmetric Unit

No.	Residues
1	Glu A:178	-	Pro A:179
2	Glu B:178	-	Pro B:179
3	Glu C:178	-	Pro C:179
4	Glu D:178	-	Pro D:179

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

(no "PROSITE Motif" information available for 3OXN)

(no "Exon" information available for 3OXN)

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:213
 aligned with Q87TP2_VIBPA | Q87TP2 from UniProtKB/TrEMBL  Length:330

    Alignment length:215
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320     
         Q87TP2_VIBPA   111 PQQCDQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDGVKALIEQALIDKPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIAKRIE 325
               SCOP domains d3oxna_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeee...eeeeee..hhhhhh..hhhhhhh.eeee...hhhhhhhhhhhh......eeeee...hhhhhhhh--...eeeeehhhhhhhhhhh.eeee..........eeeeee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oxn A 111 PQQCDQTFTIATTDYAmQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEmSLDDYLSHPHAmIAISDGVKALIEQALIDKPQRKmVLRAYHLEAALAIV--LPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSmIWHARCEHSPAQEWLRSVVREECSRLIAKRIE 325
                                   120      |130       140       150       160       170       180       190       200    |  210      |220       230       240       250   |  |260       270       280       290  |    300       310       320     
                                          127-MSE                                                                       205-MSE     217-MSE                240-MSE       254  |                                 293-MSE                            
                                                                                                                                                                            257

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q87TP2_VIBPA | Q87TP2 from UniProtKB/TrEMBL  Length:330

    Alignment length:215
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319     
         Q87TP2_VIBPA   110 DPQQCDQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDGVKALIEQALIDKPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIAKRI 324
               SCOP domains d3oxnb_ B: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh....eeee.........eeeeee...eeeeee..hhhhhh..hhhhhh...eee...hhhhhhhhhhhh.........ee...hhhhhhhhh....eeeeehhhhhhhhh...ee............eeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oxn B 110 DPQQCDQTFTIATTDYAmQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEmSLDDYLSHPHAmIAISDGVKALIEQALIDKPQRKmVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSmIWHARCEHSPAQEWLRSVVREECSRLIAKRI 324
                                   119       129       139       149       159       169       179       189       199     | 209       219       229       239|      249       259       269       279       289   |   299       309       319     
                                           127-MSE                                                                       205-MSE     217-MSE                240-MSE                                              293-MSE

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with Q87TP2_VIBPA | Q87TP2 from UniProtKB/TrEMBL  Length:330

    Alignment length:215
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318     
         Q87TP2_VIBPA   109 FDPQQCDQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDGVKALIEQALIDKPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIAKR 323
               SCOP domains d3oxnc_ C: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh....eeee...--....eeeeeeee.eeeeee..hhhhh...hhhhhh...eeee..hhhhhhhhhhhh.......eeeee.....hhhhhh....eeeeehhhhhhhhh...eeeee.......eeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oxn C 109 FDPQQCDQTFTIATTDYAmQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPT--VEPLRSEILGRVGVLCLLSKQHPLANQEmSLDDYLSHPHAmIAISDGVKALIEQALIDKPQRKmVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSmIWHARCEHSPAQEWLRSVVREECSRLIAKR 323
                                   118       128       138       148       158       168     | 178       188       198      |208       218       228       238 |     248       258       268       278       288    |  298       308       318     
                                            127-MSE                                        174  |                         205-MSE     217-MSE                240-MSE                                              293-MSE                          
                                                                                              177

Chain D from PDB  Type:PROTEIN  Length:212
 aligned with Q87TP2_VIBPA | Q87TP2 from UniProtKB/TrEMBL  Length:330

    Alignment length:212
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
         Q87TP2_VIBPA   111 PQQCDQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEMSLDDYLSHPHAMIAISDGVKALIEQALIDKPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSMIWHARCEHSPAQEWLRSVVREECSRLIAK 322
               SCOP domains d3oxnd_ D: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -LysR_substrate-3oxnD01 D:112-317                                                                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) -LysR_substrate-3oxnD02 D:112-317                                                                                                                                                                              ----- Pfam domains (2)
           Pfam domains (3) -LysR_substrate-3oxnD03 D:112-317                                                                                                                                                                              ----- Pfam domains (3)
           Pfam domains (4) -LysR_substrate-3oxnD04 D:112-317                                                                                                                                                                              ----- Pfam domains (4)
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee.........eeeeeeee.eeeeee..hhhhh...hhhhhhhh.eeee..hhhhhhhhhhhh.......eeeee.hhhhhhhhhh....eeeeehhhhhhhhhhhheeeee.......eeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oxn D 111 PQQCDQTFTIATTDYAmQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVLCLLSKQHPLANQEmSLDDYLSHPHAmIAISDGVKALIEQALIDKPQRKmVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTPFDYSmIWHARCEHSPAQEWLRSVVREECSRLIAK 322
                                   120      |130       140       150       160       170       180       190       200    |  210      |220       230       240       250       260       270       280       290  |    300       310       320  
                                          127-MSE                                                                       205-MSE     217-MSE                240-MSE                                              293-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) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: automated matches (267)

Protein domain: automated matches (267)

Vibrio parahaemolyticus [TaxId: 670] (1)

1a	d3oxna_	A:
1b	d3oxnb_	B:
1c	d3oxnc_	C:
1d	d3oxnd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: LysR_substrate (13)

Vibrio parahaemolyticus (1)

1a	LysR_substrate-3oxnD01	D:112-317
1b	LysR_substrate-3oxnD02	D:112-317
1c	LysR_substrate-3oxnD03	D:112-317
1d	LysR_substrate-3oxnD04	D:112-317

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q87TP2_VIBPA | Q87TP2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:178 - Pro A:179	[ RasMol ]
		Glu B:178 - Pro B:179	[ RasMol ]
		Glu C:178 - Pro C:179	[ RasMol ]
		Glu D:178 - Pro D:179	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 21)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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