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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PRIB

Authors :   S. Shioi, T. Ose, K. Maenaka, Y. Abe, D. Kohda, T. Katayama, T. Ueda

Date :   13 Aug 04 (Deposition) - 25 Jan 05 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Oligonucleotide Binding Fold, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Shioi, T. Ose, K. Maenaka, M. Shiroishi, Y. Abe, D. Kohda, T. Katayama, T. Ueda
Crystal Structure Of A Biologically Functional Form Of Prib From Escherichia Coli Reveals A Potential Single-Stranded Dna-Binding Site
Biochem. Biophys. Res. Commun. V. 326 766 2005
PubMed-ID: 15607735 | Reference-DOI: 10.1016/J.BBRC.2004.11.104

Molecule 1 - PRIMOSOMAL REPLICATION PROTEIN N
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PRIMOSOMAL PROTEIN B, PRIB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1WOC)

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

(no "Cis Peptide Bond" information available for 1WOC)

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

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

(no "Exon" information available for 1WOC)

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:99
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:99
                                    11        21        31        41        51        61        71        81        91         
           PRIB_ECOLI     2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI 100
               SCOP domains d1woca_ A: automated matches                                                                        SCOP domains
               CATH domains 1wocA00 A:2-100 Nucleic acid-binding proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhh....eeeeeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1woc A   2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQmPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKmVLHAEQIELI 100
                                    11        21        31        41        51        61        71        81        91         
                                                                           50-MSE                                  90-MSE

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:99
                                    11        21        31        41        51        61        71        81        91         
           PRIB_ECOLI     2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI 100
               SCOP domains d1wocb_ B: automated matches                                                                        SCOP domains
               CATH domains 1wocB00 B:2-100 Nucleic acid-binding proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee...hhhhhh......eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1woc B   2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQmPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKmVLHAEQIELI 100
                                    11        21        31        41        51        61        71        81        91         
                                                                           50-MSE                                  90-MSE

Chain C from PDB  Type:PROTEIN  Length:100
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:100
                                    11        21        31        41        51        61        71        81        91       101
           PRIB_ECOLI     2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELID 101
               SCOP domains d1wocc_ C: automated matches                                                                         SCOP domains
               CATH domains 1wocC00 C:2-101 Nucleic acid-binding proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhh......eeeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1woc C   2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQmPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKmVLHAEQIELID 101
                                    11        21        31        41        51        61        71        81        91       101
                                                                           50-MSE                                  90-MSE

Chain D from PDB  Type:PROTEIN  Length:99
 aligned with PRIB_ECOLI | P07013 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:99
                                    11        21        31        41        51        61        71        81        91         
           PRIB_ECOLI     2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI 100
               SCOP domains d1wocd_ D: automated matches                                                                        SCOP domains
               CATH domains 1wocD00 D:2-100 Nucleic acid-binding proteins                                                       CATH domains
           Pfam domains (1) SSB-1wocD01 D:2-100                                                                                 Pfam domains (1)
           Pfam domains (2) SSB-1wocD02 D:2-100                                                                                 Pfam domains (2)
           Pfam domains (3) SSB-1wocD03 D:2-100                                                                                 Pfam domains (3)
           Pfam domains (4) SSB-1wocD04 D:2-100                                                                                 Pfam domains (4)
         Sec.struct. author .eeeeeeeeeeeeeeeee.....eeeeeeeeeeee........eeeeeeeeeee.....hhhhhh....eeeeeeeeeee.......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1woc D   2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQmPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKmVLHAEQIELI 100
                                    11        21        31        41        51        61        71        81        91         
                                                                           50-MSE                                  90-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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Single strand DNA-binding domain, SSB (96)

Protein domain: automated matches (30)

Escherichia coli K-12 [TaxId: 83333] (3)

1a	d1woca_	A:
1b	d1wocb_	B:
1c	d1wocc_	C:
1d	d1wocd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (1)

1a	1wocC00	C:2-101
1b	1wocA00	A:2-100
1c	1wocB00	B:2-100
1d	1wocD00	D:2-100

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: SSB (18)

Escherichia coli (strain K12) (4)

1a	SSB-1wocD01	D:2-100
1b	SSB-1wocD02	D:2-100
1c	SSB-1wocD03	D:2-100
1d	SSB-1wocD04	D:2-100

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PRIB_ECOLI | P07013)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006270	DNA replication initiation	The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
	GO:0006269	DNA replication, synthesis of RNA primer	The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
	GO:0006276	plasmid maintenance	The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
cellular component
	GO:1990077	primosome complex	Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.
	GO:0030894	replisome	A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.

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	PRIB_ECOLI \| P07013	:	1txy 1v1q 2ccz 2pnh

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Description

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Ligands, Modified Residues, Ions (1, 8)

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