1XRX - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A DNA-BINDING PROTEIN

Authors :   A. Guarne, T. Brendler, Q. Zhao, R. Ghirlando, S. Austin, W. Yang

Date :   16 Oct 04 (Deposition) - 10 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Protein Filament, Left-Handed Helix, Dna Replication Inhibitor, Replication Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Guarne, T. Brendler, Q. Zhao, R. Ghirlando, S. Austin, W. Yang
Crystal Structure Of A Seqa-N Filament: Implications For Dn Replication And Chromosome Organization.
Embo J. V. 24 1502 2005
PubMed-ID: 15933720 | Reference-DOI: 10.1038/SJ.EMBOJ.7600634

Molecule 1 - SEQA PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	SEQA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	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 (2, 9)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 16)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:545 , HOH B:92 , HOH C:78 , HOH C:96 , HOH C:99	BINDING SITE FOR RESIDUE CA A 501

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

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

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

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

(no "Exon" information available for 1XRX)

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:35
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOL6    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxa1 A:1-35 SeqA                 SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx A  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain A from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOLI    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxa1 A:1-35 SeqA                 SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx A  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain A from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_SHIFL    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxa1 A:1-35 SeqA                 SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx A  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOL6    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxb_ B: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx B  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOLI    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxb_ B: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx B  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_SHIFL    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxb_ B: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx B  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain C from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOL6    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxc_ C: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx C  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain C from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOLI    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxc_ C: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx C  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain C from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_SHIFL    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxc_ C: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx C  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain D from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOL6 | P0AFY9 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOL6    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxd_ D: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) SeqA-1xrxD01 D:1-35                 Pfam domains (1)
           Pfam domains (2) SeqA-1xrxD02 D:1-35                 Pfam domains (2)
           Pfam domains (3) SeqA-1xrxD03 D:1-35                 Pfam domains (3)
           Pfam domains (4) SeqA-1xrxD04 D:1-35                 Pfam domains (4)
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx D  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain D from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_ECOLI    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxd_ D: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) SeqA-1xrxD01 D:1-35                 Pfam domains (1)
           Pfam domains (2) SeqA-1xrxD02 D:1-35                 Pfam domains (2)
           Pfam domains (3) SeqA-1xrxD03 D:1-35                 Pfam domains (3)
           Pfam domains (4) SeqA-1xrxD04 D:1-35                 Pfam domains (4)
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx D  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-MSE

Chain D from PDB  Type:PROTEIN  Length:35
 aligned with SEQA_SHIFL | P0AFZ0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:35
                                    10        20        30     
            SEQA_SHIFL    1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKF 35
               SCOP domains d1xrxd_ D: SeqA                     SCOP domains
               CATH domains ----------------------------------- CATH domains
           Pfam domains (1) SeqA-1xrxD01 D:1-35                 Pfam domains (1)
           Pfam domains (2) SeqA-1xrxD02 D:1-35                 Pfam domains (2)
           Pfam domains (3) SeqA-1xrxD03 D:1-35                 Pfam domains (3)
           Pfam domains (4) SeqA-1xrxD04 D:1-35                 Pfam domains (4)
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                  1xrx D  1 mKTIEVDDELYSYIASHTKHIGESASDILRRmLKF 35
                            |       10        20        30 |   
                            |                             32-MSE
                            1-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 alpha proteins (14657)

Fold: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: SeqA N-terminal domain-like (1)

Protein domain: SeqA (1)

Escherichia coli [TaxId: 562] (1)

1a	d1xrxa1	A:1-35
1b	d1xrxb_	B:
1c	d1xrxc_	C:
1d	d1xrxd_	D:

(no "CATH Domain" information available for 1XRX)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SeqA] (2)

Family: SeqA (2)

Escherichia coli O6 (2)

1a	SeqA-1xrxD01	D:1-35
1b	SeqA-1xrxD02	D:1-35
1c	SeqA-1xrxD03	D:1-35
1d	SeqA-1xrxD04	D:1-35

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SEQA_SHIFL | P0AFZ0)

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:0008156	negative regulation of DNA replication	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
	GO:0032297	negative regulation of DNA-dependent DNA replication initiation	Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B,C,D (SEQA_ECOLI | P0AFY8)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	GO:0010385	double-stranded methylated DNA binding	Interacting selectively and non-covalently with double-stranded methylated DNA. Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
	GO:0044729	hemi-methylated DNA-binding	Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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).
biological process
	GO:0008156	negative regulation of DNA replication	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
	GO:0032297	negative regulation of DNA-dependent DNA replication initiation	Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
	GO:0090143	nucleoid organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleoid. The nucleoid is the region of a bacterial cell, virion, mitochondrion or chloroplast to which the DNA is confined.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007062	sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
	GO:1990097	SeqA-DNA complex	A protein-DNA complex that contains an oligomer of SeqA bound to GATC sites in methylated or newly-synthesized, hemi-methylated double-stranded DNA, with preference for the latter. Binding of SeqA to hemimethylated DNA sequesters oriC, prevents re-methylation of DNA by Dam and in turn stops premature re-initiation of replication during one replication cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A,B,C,D (SEQA_ECOL6 | P0AFY9)

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:0008156	negative regulation of DNA replication	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
	GO:0032297	negative regulation of DNA-dependent DNA replication initiation	Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xrx)

Biological Units
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Access by PDB/NDB ID
	1xrx
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Access by UniProt ID/Accession number
	SEQA_ECOL6 \| P0AFY9
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	SEQA_ECOLI \| P0AFY8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SEQA_SHIFL \| P0AFZ0
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	SEQA_ECOL6 \| P0AFY9
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	SEQA_ECOLI \| P0AFY8
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	SEQA_SHIFL \| P0AFZ0
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UniProtKB/Swiss-Prot
	SEQA_ECOL6 \| P0AFY9	:	1iu3 1j3e 1lrr
	SEQA_ECOLI \| P0AFY8	:	1iu3 1j3e 1lrr 2ch3 3fmt
	SEQA_SHIFL \| P0AFZ0	:	1iu3 1j3e 1lrr

1lrr	SEQA DNA BINDING DOMAIN COMPLEXED WITH HEMIMETHYLATED DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (15, 25)

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File