2B7X - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   SEQUENTIAL REORGANIZATION OF BETA-SHEET TOPOLOGY BY INSERTION OF A SINGLE STRAND

Authors :   M. Sagermann, B. W. Matthews

Date :   05 Oct 05 (Deposition) - 01 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Sequence Duplication, Protein Design, Structural Switches, Tandem Repeat, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sagermann, W. A. Baase, B. W. Matthews
Sequential Reorganization Of Beta-Sheet Topology By Insertion Of A Single Strand.
Protein Sci. V. 15 1085 2006
PubMed-ID: 16597830 | Reference-DOI: 10.1110/PS.052018006
(for further references see the PDB file header)

Molecule 1 - LYSOZYME
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHS1403
	Expression System Strain	:	RR1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	E
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:142 , ARG A:143 , TRP A:144 , SER D:142 , ARG D:143	BINDING SITE FOR RESIDUE SO4 D 801
2	AC2	SOFTWARE	ASN A:146 , PHE D:120 , ASN D:122 , SER D:123 , ASN D:138	BINDING SITE FOR RESIDUE SO4 D 802
3	AC3	SOFTWARE	THR D:148 , PRO D:149 , ASN D:150 , ARG D:151	BINDING SITE FOR RESIDUE SO4 D 803
4	AC4	SOFTWARE	SER B:142 , ARG B:143 , SER C:142 , ARG C:143 , TRP C:144	BINDING SITE FOR RESIDUE SO4 C 804
5	AC5	SOFTWARE	THR C:148 , PRO C:149 , ASN C:150 , ARG C:151	BINDING SITE FOR RESIDUE SO4 C 805
6	AC6	SOFTWARE	ASN B:146 , PHE C:120 , ASN C:122 , SER C:123 , ASN C:138	BINDING SITE FOR RESIDUE SO4 C 806
7	AC7	SOFTWARE	GLN A:147 , THR A:148 , PRO A:149 , ASN A:150	BINDING SITE FOR RESIDUE SO4 A 807
8	AC8	SOFTWARE	GLY A:119 , PHE A:120 , THR A:121 , ASN A:122 , SER A:123 , ASN A:138 , ASN D:146	BINDING SITE FOR RESIDUE SO4 A 808

(no "SS Bond" information available for 2B7X)

(no "Cis Peptide Bond" information available for 2B7X)

(no "SAP(SNP)/Variant" information available for 2B7X)

(no "PROSITE Motif" information available for 2B7X)

(no "Exon" information available for 2B7X)

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:157
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains d2b7xa_ A: Phage T4 lysozyme                                                                                                                                       SCOP domains
               CATH domains 2b7xA00 A:1-168  [code=1.10.530.     40, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeee.....eeee....-----hhhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b7x A   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGYT-----SLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 168
                                    10        20        30 |     |46        56        66        76        86        96       106       116       126       136       146       156       166  
                                                          32    44

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains d2b7xb_ B: Phage T4 lysozyme                                                                                                                                       SCOP domains
               CATH domains 2b7xB00 B:1-168  [code=1.10.530.     40, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeeee...eeeee....-----hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhh.......hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b7x B   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGYT-----SLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 168
                                    10        20        30 |     |46        56        66        76        86        96       106       116       126       136       146       156       166  
                                                          32    44

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains d2b7xc_ C: Phage T4 lysozyme                                                                                                                                       SCOP domains
               CATH domains 2b7xC00 C:1-168  [code=1.10.530.     40, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh....................-----hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b7x C   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGYT-----SLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 168
                                    10        20        30 |     |46        56        66        76        86        96       106       116       126       136       146       156       166  
                                                          32    44

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains d2b7xd_ D: Phage T4 lysozyme                                                                                                                                       SCOP domains
               CATH domains 2b7xD00 D:1-168  [code=1.10.530.4  0, no name defined]                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeee.......eee.....--..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b7x D   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGYTI--SPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 168
                                    10        20        30  |  |  46        56        66        76        86        96       106       116       126       136       146       156       166  
                                                           33 42

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

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: Phage lysozyme (550)

Protein domain: Phage T4 lysozyme (546)

Bacteriophage T4 [TaxId: 10665] (546)

1a	d2b7xa_	A:
1b	d2b7xb_	B:
1c	d2b7xc_	C:
1d	d2b7xd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.40, no name defined] (526)

Enterobacteria phage t4. Organism_taxid: 10665. (237)

1a	2b7xD00	D:1-168
1b	2b7xA00	A:1-168
1c	2b7xB00	B:1-168
1d	2b7xC00	C:1-168

(no "Pfam Domain" information available for 2B7X)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ENLYS_BPT4 | P00720)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
	GO:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.

Asymmetric Unit
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1oyu	SEQUENCE DUPLICATION OF HELIX B OF T4 LYSOZYME.
1p56	RELOCATION AND DUPLICATION OF THE C-TERMINAL HELIX OF T4 LYSOZYME.
261l	SEQUENCE DUPLICATION OF HELIX B OF T4 LYSOZYME.
262l	SEQUENCE DUPLICATION OF HELIX B OF T4 LYSOZYME.
2b7w

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

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