3BKT - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   COPPER-BOUND C-TERMINAL DOMAIN OF NIKR

Authors :   C. M. Phillips, E. R. Schreiter, C. L. Drennan

Date :   07 Dec 07 (Deposition) - 19 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Nikr, Nickel Regulatory Protein, Transcription Factor, Beta Sandwich, Dna-Binding, Metal-Binding, Repressor, Transcription Regulation, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Phillips, E. R. Schreiter, Y. Guo, S. C. Wang, D. B. Zamble, C. L. Drennan
Structural Basis Of The Metal Specificity For Nickel Regulatory Protein Nikr.
Biochemistry V. 47 1938 2008
PubMed-ID: 18193897 | Reference-DOI: 10.1021/BI702006H
(for further references see the PDB file header)

Molecule 1 - NICKEL-RESPONSIVE REGULATOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NIKR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:87 , HIS A:89 , CYS A:95 , HIS C:76	BINDING SITE FOR RESIDUE CU A 2
2	AC2	SOFTWARE	HIS B:87 , HIS B:89 , CYS B:95 , VAL D:72 , HIS D:76	BINDING SITE FOR RESIDUE CU B 4
3	AC3	SOFTWARE	VAL A:72 , HIS A:76 , HIS C:87 , HIS C:89 , CYS C:95	BINDING SITE FOR RESIDUE CU C 1
4	AC4	SOFTWARE	VAL B:72 , HIS B:76 , HIS D:87 , HIS D:89 , CYS D:95	BINDING SITE FOR RESIDUE CU D 3

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

(no "Cis Peptide Bond" information available for 3BKT)

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

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

(no "Exon" information available for 3BKT)

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:83
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:83
                                    59        69        79        89        99       109       119       129   
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d3bkta_ A: Nickel responsive regulator NikR, C-terminal domain                      SCOP domains
               CATH domains 3bktA00 A:50-132 ACT-like. Chain A, domain 2                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 3bkt A  50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    59        69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:83
                                    59        69        79        89        99       109       119       129   
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d3bktb_ B: Nickel responsive regulator NikR, C-terminal domain                      SCOP domains
               CATH domains 3bktB00 B:50-132 ACT-like. Chain A, domain 2                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 3bkt B  50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    59        69        79        89        99       109       119       129

Chain C from PDB  Type:PROTEIN  Length:82
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:82
                                    60        70        80        90       100       110       120       130  
           NIKR_ECOLI    51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
               SCOP domains d3bktc_ C: Nickel responsive regulator NikR, C-terminal domain                     SCOP domains
               CATH domains 3bktC00 C:51-132 ACT-like. Chain A, domain 2                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeehhhhhhhhhhhhhh....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3bkt C  51 QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE 132
                                    60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:79
 aligned with NIKR_ECOLI | P0A6Z6 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:82
                                    59        69        79        89        99       109       119       129  
           NIKR_ECOLI    50 TQGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
               SCOP domains d3bktd_ D: Nic   kel responsive regulator NikR, C-terminal domain                  SCOP domains
               CATH domains 3bktD00 D:50-1   31 ACT-like. Chain A, domain 2                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..---hhhhhhhhhhh....eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3bkt D  50 TQGFAVLSYVYEHE---LASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLPK 131
                                    59   |   |69        79        89        99       109       119       129  
                                        63  67

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: ACT-like (63)

Family: Nickel responsive regulator NikR, C-terminal domain (14)

Protein domain: Nickel responsive regulator NikR, C-terminal domain (12)

Escherichia coli [TaxId: 562] (8)

1a	d3bkta_	A:
1b	d3bktb_	B:
1c	d3bktc_	C:
1d	d3bktd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: ACT-like. Chain A, domain 2 (9)

Escherichia coli. Organism_taxid: 562. (6)

1a	3bktD00	D:50-131
1b	3bktC00	C:51-132
1c	3bktA00	A:50-132
1d	3bktB00	B:50-132

(no "Pfam Domain" information available for 3BKT)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NIKR_ECOLI | P0A6Z6)

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.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0010045	response to nickel cation	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 nickel cation stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bkt)

Biological Units
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	3bkt
		Family and Domain Information	:	ProDom \| SYSTERS
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	NIKR_ECOLI \| P0A6Z6
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UniProtKB/Swiss-Prot
	NIKR_ECOLI \| P0A6Z6	:	1q5v 1q5y 2hza 2hzv 3bkf 3bku 3od2

3bkf	ZN-BOUND C-TERMINAL DOMAIN OF NIKR
3bku	APO C-TERMINAL DOMAIN OF NIKR

Description

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Ligands, Modified Residues, Ions (1, 4)

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