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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE AT 1.50 A OF AN OMPR/PHOB HOMOLOG FROM THERMOTOGA MARITIMA

Authors :   D. R. Buckler, Y. Zhou, A. M. Stock

Date :   28 Nov 01 (Deposition) - 05 Dec 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Dna-Binding Protein, Alph-Beta Sandwich, Winged-Helix, Helix-Turn- Helix, Response Regulator, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Buckler, Y. Zhou, A. M. Stock
Evidence Of Intradomain And Interdomain Flexibility In An Ompr/Phob Homolog From Thermotoga Maritima.
Structure V. 10 153 2002
PubMed-ID: 11839301 | Reference-DOI: 10.1016/S0969-2126(01)00706-7

Molecule 1 - DNA BINDING RESPONSE REGULATOR D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDRRD
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DRRD
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	DRRD

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 14)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	6	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:116 , ARG A:119 , ARG A:120 , TYR A:144 , GLY A:146 , SER A:147	BINDING SITE FOR RESIDUE SCN A 301
2	AC2	SOFTWARE	VAL A:90 , HOH A:316 , HOH A:333 , HOH A:338	BINDING SITE FOR RESIDUE SCN A 302
3	AC3	SOFTWARE	ARG A:12 , ASP A:16 , TYR A:33 , ASN A:168 , ARG A:223 , HOH A:311	BINDING SITE FOR RESIDUE SCN A 303
4	AC4	SOFTWARE	MSE A:39 , TYR A:40 , ASN A:44 , HOH A:406	BINDING SITE FOR RESIDUE SCN A 304
5	AC5	SOFTWARE	ARG A:12 , HIS A:213 , ARG A:223 , GLU A:225 , HOH A:426	BINDING SITE FOR RESIDUE SCN A 305
6	AC6	SOFTWARE	ALA A:21 , LYS A:24 , HOH A:502	BINDING SITE FOR RESIDUE SCN A 306

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:103	-	Pro A:104

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

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

(no "Exon" information available for 1KGS)

Asymmetric/Biological 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:219
 aligned with Q9WYN0_THEMA | Q9WYN0 from UniProtKB/TrEMBL  Length:225

    Alignment length:224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
         Q9WYN0_THEMA     2 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKSESKSTKLVCGDLILDTATKKAYRGSKEIDLTKKEYQILEYLVMNKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDKGFKKKIIHTVRGIGYVARDE 225
               SCOP domains d1kgsa2 A:2-123 PhoB receiver domain                                                                                      d1kgsa1 A:124-225 PhoB                                                                                 SCOP domains
               CATH domains 1kgsA01 A:2-122  [code=3.40.50.2300, no name defined]                                                                    1kgsA02 A:123-225 'winged helix' repressor DNA binding doma     in                                      CATH domains
               Pfam domains ---Response_reg-1kgsA01 A:5-115                                                                                   ------------------------------Trans_reg_C-1kgsA02 A:146-222                                                --- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhh.....eeeee..hhhhhhhhh......eeee...hhhhhhhhhhhhhhhhh.....eeee..eeee....eeee..eee..hhhhhhhhhhhhhh....eehhhhhhhh.-----hhhhhhhhhhhhhhhhhhh......eeee...eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgs A   2 NVRVLVVEDERDLADLITEALKKEmFTVDVCYDGEEGmYmALNEPFDVVILDImLPVHDGWEILKSmRESGVNTPVLmLTALSDVEYRVKGLNmGADDYLPKPFDLRELIARVRALIRRKSESKSTKLVCGDLILDTATKKAYRGSKEIDLTKKEYQILEYLVmNKNRVVTKEELQEHLW-----VFSDVLRSHIKNLRKKVDKGFKKKIIHTVRGIGYVARDE 225
                                    11        21    |   31       |41        51   |    61      | 71       |81        91   |   101       111       121       131       141       151       161   |   171       181     | 191       201       211       221    
                                                   26-MSE       39-MSE          55-MSE       68-MSE     79-MSE          95-MSE                                                               165-MSE         181   187                                      
                                                                  41-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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: C-terminal effector domain of the bipartite response regulators (45)

Family: PhoB-like (13)

Protein domain: PhoB (5)

Thermotoga maritima [TaxId: 2336] (1)

d1kgsa1

A:124-225

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

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: CheY-related (166)

Protein domain: PhoB receiver domain (2)

Thermotoga maritima [TaxId: 2336] (1)

d1kgsa2

A:2-123

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Thermotoga maritima. Organism_taxid: 2336. (8)

1kgsA01

A:2-122

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Thermotoga maritima. Organism_taxid: 2336. (11)

1kgsA02

A:123-225

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: Response_reg (94)

Thermotoga maritima (9)

Response_reg-1kgsA01

A:5-115

Clan: HTH (544)

Family: Trans_reg_C (13)

Thermotoga maritima (2)

Trans_reg_C-1kgsA02

A:146-222

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9WYN0_THEMA | Q9WYN0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	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.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys A:103 - Pro A:104	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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