2F97 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   EFFECTOR BINDING DOMAIN OF BENM (CRYSTALS GENERATED FROM HIGH PH CONDITIONS)

Authors :   O. C. Ezezika, S. Haddad, E. L. Neidle, C. Momany

Date :   05 Dec 05 (Deposition) - 19 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Benm, Lysr-Type Regulator, Tetramerization, Effector Binding Domain, Inducer Binding Domain, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. C. Ezezika, S. Haddad, E. L. Neidle, C. Momany
Oligomerization Of Benm, A Lysr-Type Transcriptional Regulator: Structural Basis For The Aggregation Of Proteins In This Family.
Acta Crystallogr. , Sect. F V. 63 361 2007
PubMed-ID: 17565172 | Reference-DOI: 10.1107/S1744309107019185
(for further references see the PDB file header)

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	DE3(BL21)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BENM, BENR
	Organism Scientific	:	ACINETOBACTER BAYLYI
	Organism Taxid	:	202950
	Strain	:	ADP1
	Synonym	:	BEN AND CAT OPERON TRANSCRIPTIONAL REGULATOR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	4	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:105 , ILE A:108 , PHE A:144 , LEU A:159 , TYR A:293 , HOH A:1014	BINDING SITE FOR RESIDUE ACT A 1003
2	AC2	SOFTWARE	GLY A:98 , GLU A:125 , MET A:126 , GLY A:127 , SER A:197 , SER A:198 , PRO A:199 , ARG A:225 , HOH A:1135 , HOH A:1164	BINDING SITE FOR RESIDUE PG4 A 1001
3	AC3	SOFTWARE	ARG A:93 , TYR A:124 , GLY A:138 , ARG A:139 , HOH A:1118	BINDING SITE FOR RESIDUE PG4 A 1002
4	AC4	SOFTWARE	HIS A:116 , TYR A:283	BINDING SITE FOR RESIDUE PEG A 1004
5	AC5	SOFTWARE	LYS A:155 , ASN A:275 , GLU A:277 , TYR A:286 , TRP A:304	BINDING SITE FOR RESIDUE PEG A 1005

(no "SS Bond" information available for 2F97)

Asymmetric Unit

No.	Residues
1	Tyr A:195	-	Pro A:196
2	Lys A:200	-	Pro A:201

(no "SAP(SNP)/Variant" information available for 2F97)

(no "PROSITE Motif" information available for 2F97)

(no "Exon" information available for 2F97)

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:216
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:216
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298      
           BENM_ACIAD    89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW 304
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhh..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhhh...eee.......hhhhhhhhhhhhh......eee..hhhhhhhhhhh...eeeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f97 A  89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW 304
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

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 '\|'

(no "SCOP Domain" information available for 2F97)

(no "CATH Domain" information available for 2F97)

(no "Pfam Domain" information available for 2F97)

Asymmetric Unit(hide GO term definitions)

Chain A (BENM_ACIAD | O68014)

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:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	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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	Ligands, Modified Residues, Ions
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		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:200 - Pro A:201	[ RasMol ]
		Tyr A:195 - Pro A:196	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2f97
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	BENM_ACIAD \| O68014	:	2f6g 2f6p 2f78 2f7a 2f8d 2h99 2h9b 3k1m 3k1n 3k1p 3m1e 4ihs 4iht

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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