2NP2 | PD0903 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   HBB-DNA COMPLEX

Authors :   P. A. Rice, K. W. Mouw

Date :   26 Oct 06 (Deposition) - 27 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.02

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Protein-Dna Complex, Dna-Binding Protein, Dna-Bending Protein, Dnabii Family, Hu/Ihf Family, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. W. Mouw, P. A. Rice
Shaping The Borrelia Burgdorferi Genome: Crystal Structure And Binding Properties Of The Dna-Bending Protein Hbb.
Mol. Microbiol. V. 63 1319 2007
PubMed-ID: 17244195 | Reference-DOI: 10.1111/J.1365-2958.2007.05586.X
(for further references see the PDB file header)

Molecule 1 - 36-MER
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - HBB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HBB
	Organism Common	:	LYME DISEASE SPIROCHETE
	Organism Scientific	:	BORRELIA BURGDORFERI
	Organism Taxid	:	139

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NP2)

(no "Site" information available for 2NP2)

(no "SS Bond" information available for 2NP2)

(no "Cis Peptide Bond" information available for 2NP2)

Asymmetric/Biological Unit (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DBH_BORBU_002 *	V	9	I	DBH_BORBU	---	---	A/B	V	9	I
2	UniProt	VAR_DBH_BORBU_003 *	S	19	A	DBH_BORBU	---	---	A/B	A	19	A
3	UniProt	VAR_DBH_BORBU_004 *	K	23	R	DBH_BORBU	---	---	A/B	K	23	R
4	UniProt	VAR_DBH_BORBU_005 *	Y	33	C	DBH_BORBU	---	---	A/B	Y	33	C
5	UniProt	VAR_DBH_BORBU_006 *	V	65	L	DBH_BORBU	---	---	A/B	V	65	L
6	UniProt	VAR_DBH_BORBU_007 *	K	69	R	DBH_BORBU	---	---	A/B	K	69	R
7	UniProt	VAR_DBH_BORBU_008 *	E	81	V	DBH_BORBU	---	---	A/B	E	81	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_LIKE	PS00045	Bacterial histone-like DNA-binding proteins signature.	DBH_BORBU	59-79	2	A:59-79 B:59-79

(no "Exon" information available for 2NP2)

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:102
 aligned with DBH_BORBU | Q57267 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:102
                                    15        25        35        45        55        65        75        85        95       105  
            DBH_BORBU     6 RPKVTKSDIVDQISLNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
               SCOP domains d2np2a_ A: automated matches                                                                           SCOP domains
               CATH domains 2np2A00 A:6-107 HU Protein, subunit A                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeeee...................eeeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---I---------A---R---------C-------------------------------L---R-----------V-------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HISTONE_LIKE         ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2np2 A   6 RPKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
                                    15        25        35        45        55        65        75        85        95       105

Chain A from PDB  Type:PROTEIN  Length:102
 aligned with Q3I4Z2_BORBG | Q3I4Z2 from UniProtKB/TrEMBL  Length:108

    Alignment length:102
                                    15        25        35        45        55        65        75        85        95       105  
         Q3I4Z2_BORBG     6 RPKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
               SCOP domains d2np2a_ A: automated matches                                                                           SCOP domains
               CATH domains 2np2A00 A:6-107 HU Protein, subunit A                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeeee...................eeeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---I---------A---R---------C-------------------------------L---R-----------V-------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2np2 A   6 RPKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
                                    15        25        35        45        55        65        75        85        95       105

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with DBH_BORBU | Q57267 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:102
                                    15        25        35        45        55        65        75        85        95       105  
            DBH_BORBU     6 RPKVTKSDIVDQISLNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
               SCOP domains d2np2b_ B: automated matches                                                                           SCOP domains
               CATH domains 2np2B00 B:6-107 HU Protein, subunit A                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeeee...................eeeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---I---------A---R---------C-------------------------------L---R-----------V-------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HISTONE_LIKE         ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2np2 B   6 RPKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
                                    15        25        35        45        55        65        75        85        95       105

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with Q3I4Z2_BORBG | Q3I4Z2 from UniProtKB/TrEMBL  Length:108

    Alignment length:102
                                    15        25        35        45        55        65        75        85        95       105  
         Q3I4Z2_BORBG     6 RPKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
               SCOP domains d2np2b_ B: automated matches                                                                           SCOP domains
               CATH domains 2np2B00 B:6-107 HU Protein, subunit A                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeeee...................eeeeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---I---------A---R---------C-------------------------------L---R-----------V-------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2np2 B   6 RPKVTKSDIVDQIALNIKNNNLKLEKKYIRLVIDAFFEELKSNLCSNNVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 107
                                    15        25        35        45        55        65        75        85        95       105

Chain C from PDB  Type:DNA  Length:36
                                                                    
                 2np2 C 203 GTATTTAATACTATATGTCATATAGTATTAAATACT 238
                                   212       222       232

Chain D from PDB  Type:DNA  Length:36
                                                                    
                 2np2 D 203 GTATTTAATACTATATGTCATATAGTATTAAATACT 238
                                   212       222       232

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: IHF-like DNA-binding proteins (28)

Superfamily: IHF-like DNA-binding proteins (28)

Family: automated matches (4)

Protein domain: automated matches (4)

Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] (1)

1a	d2np2a_	A:
1b	d2np2b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: HU Protein; Chain A (18)

Homologous Superfamily: HU Protein, subunit A (18)

[unclassified] (9)

1a	2np2A00	A:6-107
1b	2np2B00	B:6-107

(no "Pfam Domain" information available for 2NP2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q3I4Z2_BORBG | Q3I4Z2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.

Chain A,B (DBH_BORBU | Q57267)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2np2)

	Sites
(no "Sites" information available for 2np2)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2np2)

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	2np2
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(no "Entries Sharing at Least One Protein Chain" available for 2NP2)

1b8z	THERMATOGA MARITIMA HU PROTEIN ALONE
1ihf	E. COLI IHF BOUND TO NICKED H' DNA
1owf	MUTANT IHF (BETAE44A) BOUND TO NICKED H' DNA
1p51	ANABAENA HU BOUND TO AHU6 DNA
1p71	ANABAENA HU BOUND TO TR3 DNA
1p78	ANABAENA HU BOUND TO AHU2 DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 14)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (2, 4)

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Related Entries Specified in the PDB File