2R0Q - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF A SERINE RECOMBINASE- DNA REGULATORY COMPLEX

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

Date :   21 Aug 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H

Keywords :   Site-Specific Recombinase, Resolvase, Dna-Binding Protein, Protein-Dna Complex, Dna Integration, Dna Invertase, Dna Recombination, Plasmid, Transposable Element, Transposition, Recombination/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. W. Mouw, S. J. Rowland, M. M. Gajjar, M. R. Boocock, W. M. Stark, P. A. Rice
Architecture Of A Serine Recombinase-Dna Regulatory Complex.
Mol. Cell V. 30 145 2008
PubMed-ID: 18439894 | Reference-DOI: 10.1016/J.MOLCEL.2008.02.023
(for further references see the PDB file header)

Molecule 1 - PUTATIVE TRANSPOSON TN552 DNA-INVERTASE BIN3
	Chains	:	C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSA1122
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BIN3
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	NCTC 9789

Molecule 2 - 31-MER
	Chains	:	A, G
	Engineered	:	YES
	Other Details	:	SITE II DNA STRAND 1
	Synthetic	:	YES

Molecule 3 - 31-MER
	Chains	:	B, H
	Engineered	:	YES
	Other Details	:	SITE II DNA STRAND 2
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG C:130 , ARG D:7 , SER D:9 , SER D:10	BINDING SITE FOR RESIDUE SO4 D 210
2	AC2	SOFTWARE	ARG E:130 , ARG F:7 , SER F:9 , SER F:10	BINDING SITE FOR RESIDUE SO4 F 210

(no "SS Bond" information available for 2R0Q)

(no "Cis Peptide Bond" information available for 2R0Q)

(no "SAP(SNP)/Variant" information available for 2R0Q)

Asymmetric/Biological Unit (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECOMBINASES_3	PS51736	Resolvase/invertase-type recombinase catalytic domain profile.	BIN3_STAAU	1-143	4	C:1-143 D:1-143 E:1-143 F:1-143
2	RECOMBINASES_1	PS00397	Site-specific recombinases active site.	BIN3_STAAU	5-13	4	C:5-13 D:5-13 E:5-13 F:5-13
3	RECOMBINASES_2	PS00398	Site-specific recombinases signature 2.	BIN3_STAAU	56-68	4	C:56-68 D:56-68 E:56-68 F:56-68

(no "Exon" information available for 2R0Q)

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:DNA  Length:31
                                                               
                 2r0q A   1 AACGTATGATTAGGGTGTATATTAATTTATA  31
                                    10        20        30

Chain B from PDB  Type:DNA  Length:31
                                                               
                 2r0q B  32 TAAATTAATATACACCCTAATCATACGTTTA  62
                                    41        51        61

Chain C from PDB  Type:PROTEIN  Length:193
 aligned with BIN3_STAAU | P20384 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           BIN3_STAAU     1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEKQSGKSIENRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhh....eeee..-------.hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhh.eeee....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: C:1-143 UniProt: 1-143                                                                                                    --------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----RECOMBINA------------------------------------------RECOMBINASES_------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r0q C   1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEK-------NRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
                                    10        20        30   |     - |      50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
                                                            34      42

Chain D from PDB  Type:PROTEIN  Length:191
 aligned with BIN3_STAAU | P20384 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           BIN3_STAAU     1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEKQSGKSIENRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhh....eeee..-------.hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....--..........................hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: D:1-143 UniProt: 1-143                                                                                                    --------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----RECOMBINA------------------------------------------RECOMBINASES_------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r0q D   1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEK-------NRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESK--QAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
                                    10        20        30   |     - |      50        60        70        80        90       100       110       120        |- |     140       150       160       170       180       190       200
                                                            34      42                                                                                    129  |                                                                    
                                                                                                                                                             132

Chain E from PDB  Type:PROTEIN  Length:193
 aligned with BIN3_STAAU | P20384 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           BIN3_STAAU     1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEKQSGKSIENRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhh...eeee..-------.hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhh.eeee....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: E:1-143 UniProt: 1-143                                                                                                    --------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----RECOMBINA------------------------------------------RECOMBINASES_------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r0q E   1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEK-------NRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
                                    10        20        30   |     - |      50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
                                                            34      42

Chain F from PDB  Type:PROTEIN  Length:191
 aligned with BIN3_STAAU | P20384 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           BIN3_STAAU     1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEKQSGKSIENRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Resolvase-2r0qF05 F:2-145                                                                                                                       -HTH_7-2r0qF01 F:147-199                              - Pfam domains (1)
           Pfam domains (2) -Resolvase-2r0qF06 F:2-145                                                                                                                       -HTH_7-2r0qF02 F:147-199                              - Pfam domains (2)
           Pfam domains (3) -Resolvase-2r0qF07 F:2-145                                                                                                                       -HTH_7-2r0qF03 F:147-199                              - Pfam domains (3)
           Pfam domains (4) -Resolvase-2r0qF08 F:2-145                                                                                                                       -HTH_7-2r0qF04 F:147-199                              - Pfam domains (4)
         Sec.struct. author .eeeee........hhhhhhhhhh....eeee..-------.hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhhhh.eeee....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....--..........................hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: F:1-143 UniProt: 1-143                                                                                                    --------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----RECOMBINA------------------------------------------RECOMBINASES_------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r0q F   1 MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEK-------NRPILQKALNFVRMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLIIQILAMVSEQERNESK--QAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG 200
                                    10        20        30   |     - |      50        60        70        80        90       100       110       120        |- |     140       150       160       170       180       190       200
                                                            34      42                                                                                    129  |                                                                    
                                                                                                                                                             132

Chain G from PDB  Type:DNA  Length:31
                                                               
                 2r0q G   1 AACGTATGATTAGGGTGTATATTAATTTATA  31
                                    10        20        30

Chain H from PDB  Type:DNA  Length:31
                                                               
                 2r0q H  32 TAAATTAATATACACCCTAATCATACGTTTA  62
                                    41        51        61

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 2R0Q)

(no "CATH Domain" information available for 2R0Q)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_7 (11)

Staphylococcus aureus (1)

1a	HTH_7-2r0qF01	F:147-199
1b	HTH_7-2r0qF02	F:147-199
1c	HTH_7-2r0qF03	F:147-199
1d	HTH_7-2r0qF04	F:147-199

Clan: no clan defined [family: Resolvase] (7)

Family: Resolvase (7)

Staphylococcus aureus (2)

2a	Resolvase-2r0qF05	F:2-145
2b	Resolvase-2r0qF06	F:2-145
2c	Resolvase-2r0qF07	F:2-145
2d	Resolvase-2r0qF08	F:2-145

Asymmetric/Biological Unit(hide GO term definitions)

Chain C,D,E,F (BIN3_STAAU | P20384)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000150	recombinase activity	Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
biological process
	GO:0015074	DNA integration	The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0032196	transposition	Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r0q)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2r0q
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	BIN3_STAAU \| P20384
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	BIN3_STAAU \| P20384
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BIN3_STAAU \| P20384	:	3pkz 5c31 5c32 5c34 5c35

1gdt	GAMMA DELTA RESOLVASE DIMER BOUND TO UNCLEAVED SITE I DNA
1zr4	SYNAPTIC GAMMA DELTA RESOLVASE TETRAMER BOUND TO TWO CLEAVED SITE I DNAS
2gm4	AN ACTIVATED, TETRAMERIC GAMMA DELTA RESOLVASE:HIN CHIMERA BOUND TO TWO CLEAVED SITE I DNAS
2gm5	AN ACTIVATED TRUNCATED GAMMA DELTA RESOLVASE TETRAMER
2rsl	GAMMA DELTA RESOLVASE CATALYTIC DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 12)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 8)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File