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Title :   CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR PROTEIN, LACL FAMILY FROM RHIZOBIUM ETLI

Authors :   K. Palani, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   12 Apr 10 (Deposition) - 21 Apr 10 (Release) - 21 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.91

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

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

Reference :   K. Palani, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Transcriptional Regulator Protein, Lacl Family From Rhizobium Etli
To Be Published
PubMed: search

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REGULATOR PROTEIN, LACI FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3 (BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 50-339
	Gene	:	RHE_PE00360
	Organism Scientific	:	RHIZOBIUM ETLI
	Organism Taxid	:	347834
	Strain	:	CFN 42/ATCC 51251

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3MIZ)

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

Asymmetric Unit

No.	Residues
1	Lys A:289	-	Pro A:290
2	Thr B:72	-	Pro B:73
3	Ile B:269	-	Pro B:270
4	Lys B:289	-	Pro B:290
5	Tyr B:320	-	Pro B:321

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

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

(no "Exon" information available for 3MIZ)

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:281
 aligned with Q2K0Z9_RHIEC | Q2K0Z9 from UniProtKB/TrEMBL  Length:341

    Alignment length:281
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         Q2K0Z9_RHIEC    58 RSNTFGIITDYVSTTPYSVDIVRGIQDWANANGKTILIANTGGSSEREVEIWKMFQSHRIDGVLYVTMYRRIVDPESGDVSIPTVMINCRPQTRELLPSIEPDDYQGARDLTRYLLERGHRRIGYIRLNPILLGAELRLDAFRRTTSEFGLTENDLSISLGMDGPVGAENNYVFAAATEMLKQDDRPTAIMSGNDEMAIQIYIAAMALGLRIPQDVSIVGFDDFRTVTMALKPELTTAALPYYDLGREGAKWLNDLIAGEKIYPGSRVVSCKLVERSSAAF 338
               SCOP domains d3miza_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeee...........eeeeeee........eeeehhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhh.hhh.eeeee.ee......eehhhhhhhhhhh......eeee.hhhhhhhhhhhhhh...hhhhhheee....hhhhhh.......eee.hhhhhhhhhhhhhhhhhh.......eeee..eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3miz A  58 RSNTFGIITDYVSTTPYSVDIVRGIQDWANANGKTILIANTGGSSEREVEIWKmFQSHRIDGVLYVTmYRRIVDPESGDVSIPTVmINCRPQTRELLPSIEPDDYQGARDLTRYLLERGHRRIGYIRLNPILLGAELRLDAFRRTTSEFGLTENDLSISLGmDGPVGAENNYVFAAATEmLKQDDRPTAImSGNDEmAIQIYIAAmALGLRIPQDVSIVGFDDFRTVTmALKPELTTAALPYYDLGREGAKWLNDLIAGEKIYPGSRVVSCKLVERSSAAF 338
                                    67        77        87        97       107   |   117       127       137     | 147       157       167       177       187       197       207       217 |     227       237       247|     |257     | 267       277       287       297       307       317       327       337 
                                                                               111-MSE       125-MSE           143-MSE                                                                     219-MSE           237-MSE    248-MSE |      263-MSE                286-MSE                                                
                                                                                                                                                                                                                              254-MSE

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with Q2K0Z9_RHIEC | Q2K0Z9 from UniProtKB/TrEMBL  Length:341

    Alignment length:281
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338 
         Q2K0Z9_RHIEC    59 SNTFGIITDYVSTTPYSVDIVRGIQDWANANGKTILIANTGGSSEREVEIWKMFQSHRIDGVLYVTMYRRIVDPESGDVSIPTVMINCRPQTRELLPSIEPDDYQGARDLTRYLLERGHRRIGYIRLNPILLGAELRLDAFRRTTSEFGLTENDLSISLGMDGPVGAENNYVFAAATEMLKQDDRPTAIMSGNDEMAIQIYIAAMALGLRIPQDVSIVGFDDFRTVTMALKPELTTAALPYYDLGREGAKWLNDLIAGEKIYPGSRVVSCKLVERSSAAFG 339
               SCOP domains d3mizb_ B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-3mizB01 B:169-336                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-3mizB02 B:169-336                                                                                                                                          --- Pfam domains (2)
         Sec.struct. author ..eeeeee........hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeee...........eeeeeee........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh..hhh.eeeee.ee......eehhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eee....hhhhhh.......eee.hhhhhhhhhhhhhhhhhhh......eeee..eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3miz B  59 SNTFGIITDYVSTTPYSVDIVRGIQDWANANGKTILIANTGGSSEREVEIWKmFQSHRIDGVLYVTmYRRIVDPESGDVSIPTVmINCRPQTRELLPSIEPDDYQGARDLTRYLLERGHRRIGYIRLNPILLGAELRLDAFRRTTSEFGLTENDLSISLGmDGPVGAENNYVFAAATEmLKQDDRPTAImSGNDEmAIQIYIAAmALGLRIPQDVSIVGFDDFRTVTmALKPELTTAALPYYDLGREGAKWLNDLIAGEKIYPGSRVVSCKLVERSSAAFG 339
                                    68        78        88        98       108  |    118      |128       138    |  148       158       168       178       188       198       208       218|      228       238       248     | 258    |  268       278       288       298       308       318       328       338 
                                                                              111-MSE       125-MSE           143-MSE                                                                     219-MSE           237-MSE    248-MSE |      263-MSE                286-MSE                                                 
                                                                                                                                                                                                                             254-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 I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: automated matches (65)

Protein domain: automated matches (65)

Rhizobium etli [TaxId: 347834] (1)

1a	d3miza_	A:
1b	d3mizb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Rhizobium etli (strain CFN 42 / ATCC 51251) (1)

1a	Peripla_BP_3-3mizB01	B:169-336
1b	Peripla_BP_3-3mizB02	B:169-336

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q2K0Z9_RHIEC | Q2K0Z9)

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.

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	Sites
(no "Sites" information available for 3miz)

	Cis Peptide Bonds
		Ile B:269 - Pro B:270	[ RasMol ]
		Lys A:289 - Pro A:290	[ RasMol ]
		Lys B:289 - Pro B:290	[ RasMol ]
		Thr B:72 - Pro B:73	[ RasMol ]
		Tyr B:320 - Pro B:321	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (1, 18)

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Cis Peptide Bonds (5, 5)

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