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Biological Unit 4 (Jmol Viewer)

Title :   BACTERIOPHAGE T4 LYSOZYME MUTANT R96V IN WILDTYPE BACKGROUND AT LOW TEMPERATURE

Authors :   B. H. M. Mooers

Date :   27 Feb 08 (Deposition) - 17 Feb 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

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 :   Bacteriophage T4 Lysozyme, Viral Lysozyme, Mutational Analysis, Protein Engineering, Thermal Stability, Protein Stability, Protein Electrostatics, Protein Structure, Charge Burial, Hydrogen Bonding, Helix Dipole, Protein Crevices, Steric Strain, Temperature-Sensitive Mutant, Phosphate Binding Site, Mpd Binding Site, Chloride Binding Site, Antimicrobial, Bacteriolytic Enzyme, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. H. Mooers, W. A. Baase, J. W. Wray, B. W. Matthews
Contributions Of All 20 Amino Acids At Site 96 To The Stability And Structure Of T4 Lysozyme.
Protein Sci. V. 18 871 2009
PubMed-ID: 19384988 | Reference-DOI: 10.1002/PRO.94
(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 Common	:	VIRUS
	Organism Scientific	:	BACTERIOPHAGE T4
	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 (3, 14)

No.	Name	Count	Type	Full Name
1	HEZ	4	Ligand/Ion	HEXANE-1,6-DIOL
2	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	HEZ	1	Ligand/Ion	HEXANE-1,6-DIOL
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	HEZ	-1	Ligand/Ion	HEXANE-1,6-DIOL
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	HEZ	2	Ligand/Ion	HEXANE-1,6-DIOL
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 5)

No.	Name	Count	Type	Full Name
1	HEZ	1	Ligand/Ion	HEXANE-1,6-DIOL
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:125 , SER B:38 , LEU B:39 , ASN B:40 , HOH B:2014 , HOH B:2033 , HOH B:2047	BINDING SITE FOR RESIDUE SO4 B 1902
02	AC2	SOFTWARE	SER B:44 , LYS B:48 , PHE B:114 , THR B:115 , ASN B:116 , SER B:117 , HOH B:1955	BINDING SITE FOR RESIDUE SO4 B 1903
03	AC3	SOFTWARE	THR B:142 , PRO B:143 , ASN B:144 , ARG B:145 , HOH B:2052	BINDING SITE FOR RESIDUE SO4 B 1905
04	AC4	SOFTWARE	SER C:44 , LYS C:48 , PHE C:114 , THR C:115 , ASN C:116 , SER C:117 , ASN C:132 , HOH C:2136	BINDING SITE FOR RESIDUE SO4 C 1906
05	AC5	SOFTWARE	SER C:38 , LEU C:39 , ASN C:40 , ARG D:125 , HOH D:2136 , HOH D:2146 , HOH D:2160 , HOH D:2170	BINDING SITE FOR RESIDUE SO4 D 1901
06	AC6	SOFTWARE	THR D:142 , PRO D:143 , ASN D:144 , ARG D:145 , HOH D:2128 , HOH D:2133	BINDING SITE FOR RESIDUE SO4 D 1904
07	AC7	SOFTWARE	ASP A:89 , SER A:90 , LYS A:124 , HOH A:2103	BINDING SITE FOR RESIDUE HEZ A 1901
08	AC8	SOFTWARE	LEU C:33 , HEZ C:1922	BINDING SITE FOR RESIDUE HEZ C 1921
09	AC9	SOFTWARE	LYS C:35 , MET C:106 , HEZ C:1921	BINDING SITE FOR RESIDUE HEZ C 1922
10	BC1	SOFTWARE	ASP D:89 , LYS D:124	BINDING SITE FOR RESIDUE HEZ D 1923
11	BC2	SOFTWARE	ASP A:72 , ARG A:76 , HOH A:2064 , ILE B:3 , VAL B:75 , TYR B:88 , HOH B:1970	BINDING SITE FOR RESIDUE MPD A 1911
12	BC3	SOFTWARE	TYR A:88 , HOH A:1927 , HOH A:2068 , ASP B:72 , ARG B:76	BINDING SITE FOR RESIDUE MPD A 1914
13	BC4	SOFTWARE	ASP C:72 , ARG C:76 , TYR D:88 , HOH D:2052 , HOH D:2060	BINDING SITE FOR RESIDUE MPD D 1912
14	BC5	SOFTWARE	TYR C:88 , HOH C:2144 , VAL D:71 , ASP D:72 , ARG D:76 , HOH D:2186	BINDING SITE FOR RESIDUE MPD D 1913

(no "SS Bond" information available for 3CDO)

(no "Cis Peptide Bond" information available for 3CDO)

(no "SAP(SNP)/Variant" information available for 3CDO)

(no "PROSITE Motif" information available for 3CDO)

(no "Exon" information available for 3CDO)

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:162
 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 d3cdoa_ A: Phage T4 lysozyme                                                                                                                                       SCOP domains
               CATH domains 3cdoA00 A:1-162  [code=1.10.530.40, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cdo A   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRVCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d3cdob_ B: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 3cdoB00 B:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeee.....eeee..ee.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdo B   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRVCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d3cdoc_ C: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 3cdoC00 C:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeee.....eeee..ee.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdo C   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRVCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d3cdod_ D: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 3cdoD00 D:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdo D   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRVCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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	d3cdoa_	A:
1b	d3cdob_	B:
1c	d3cdoc_	C:
1d	d3cdod_	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)

Bacteriophage t4 (15)

1a	3cdoA00	A:1-162
1b	3cdoB00	B:1-164
1c	3cdoC00	C:1-164
1d	3cdoD00	D:1-164

(no "Pfam Domain" information available for 3CDO)

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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1l34	MUTANT R96H LYSOZYME AT ROOM TEMPERATURE
1l63	WILDTYPE T4 LYSOZYME AT ROOM TEMPERATURE
3c7w	MUTANT R96K LYSOZYME AT ROOM TEMPERATURE
3c7y	MUTANT R96A OF T4 LYSOZYME IN WILDTYPE BACKGROUND AT 298K
3c7z	MUTANT D89A/R96H LYSOZYME AT ROOM TEMPERATURE
3c80	MUTANT R96Y LYSOZYME AT ROOM TEMPERATURE
3c81	MUTANT K85A LYSOZYME AT ROOM TEMPERATURE
3c82	MUTANT K85A/R96H LYSOZYME AT ROOM
3c83	MUTANT D89A LYSOZYME AT ROOM TEMPERATURE
3c8q	MUTANT R96D LYSOZYME AT ROOM TEMPERATURE
3c8r	MUTANT R96G LYSOZYME AT ROOM TEMPERATURE
3c8s	MUTANT R96E LYSOZYME AT ROOM TEMPERATURE
3cdq	MUTANT R96S LYSOZYME AT ROOM TEMPERATURE
3cdr	MUTANT R96Q LYSOZYME AT ROOM TEMPERATURE
3cdt	MUTANT R96N LYSOZYME AT ROOM TEMPERATURE
3cdv	MUTANT R96M LYSOZYME AT ROOM TEMPERATURE
3f8v	R96H AT 1.08 ANG
3f9l	D72A AT 1.19 ANG
3fa0	WILD TYPE AT 1.09 ANG
3fad	D72A/R96H AT 1.20 ANG
3fi5	R96W AT 1.73 ANG

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 4)

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