3U0S - JenaLib

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)

Title :   CRYSTAL STRUCTURE OF AN ENZYME REDESIGNED THROUGH MULTIPLAYER ONLINE GAMING: CE6

Authors :   J. B. Bale, B. W. Shen, B. L. Stoddard

Date :   29 Sep 11 (Deposition) - 01 Feb 12 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Protein Engineering, Computer-Aided Design, Computationally-Directed Design, Multiplayer Online Gaming, Crowdsourcing, Foldit, Diels- Alder, Enzyme Design, Active Site Redesign, Substrate Specificity, Beta-Propeller, Helix-Loop-Helix, Loop Remodel, Hydrolase, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. B. Eiben, J. B. Siegel, J. B. Bale, S. Cooper, F. Khatib, B. W. Shen, F. Players, B. L. Stoddard, Z. Popovic, D. Baker
Increased Diels-Alderase Activity Through Backbone Remodeling Guided By Foldit Players.
Nat. Biotechnol. V. 30 190 2012
PubMed-ID: 22267011 | Reference-DOI: 10.1038/NBT.2109
(for further references see the PDB file header)

Molecule 1 - DIISOPROPYL-FLUOROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.8.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29B+
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DFPASE
	Mutation	:	YES
	Organism Common	:	COMMON EUROPEAN SQUID
	Organism Scientific	:	LOLIGO VULGARIS
	Organism Taxid	:	6622
	Synonym	:	DFPASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	6	Ligand/Ion	GLYCEROL
3	NA	2	Ligand/Ion	SODIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:39 , LEU A:42 , THR A:43 , GLN A:208 , LYS A:238 , TRP A:257 , HOH A:378	BINDING SITE FOR RESIDUE EPE A 338
02	AC2	SOFTWARE	PHE A:324 , GLY A:325 , PRO B:48 , TYR B:52	BINDING SITE FOR RESIDUE GOL A 339
03	AC3	SOFTWARE	LEU A:42 , LEU A:161 , LYS A:238 , PHE B:327	BINDING SITE FOR RESIDUE GOL A 340
04	AC4	SOFTWARE	PHE A:165 , HOH A:403 , LYS B:27	BINDING SITE FOR RESIDUE GOL A 341
05	AC5	SOFTWARE	TYR A:82 , ASP A:249 , ARG A:312	BINDING SITE FOR RESIDUE SO4 A 342
06	AC6	SOFTWARE	ARG A:162 , LYS B:323	BINDING SITE FOR RESIDUE SO4 A 343
07	AC7	SOFTWARE	LYS A:53 , ARG A:56 , LYS A:273 , HOH A:462	BINDING SITE FOR RESIDUE SO4 A 344
08	AC8	SOFTWARE	LEU B:42 , THR B:43 , GLN B:208 , LYS B:238 , TRP B:257 , HOH B:356 , HOH B:452	BINDING SITE FOR RESIDUE EPE B 338
09	AC9	SOFTWARE	ILE B:224 , LYS B:227	BINDING SITE FOR RESIDUE GOL B 339
10	BC1	SOFTWARE	GLU B:163	BINDING SITE FOR RESIDUE GOL B 340
11	BC2	SOFTWARE	PHE B:324	BINDING SITE FOR RESIDUE GOL B 341
12	BC3	SOFTWARE	GLU B:248 , ASP B:249 , SO4 B:344	BINDING SITE FOR RESIDUE NA B 342
13	BC4	SOFTWARE	TYR B:82 , PRO B:154 , GLN B:311 , SO4 B:344	BINDING SITE FOR RESIDUE NA B 343
14	BC5	SOFTWARE	TYR B:82 , ASP B:249 , ARG B:312 , NA B:342 , NA B:343	BINDING SITE FOR RESIDUE SO4 B 344
15	BC6	SOFTWARE	LYS A:323 , ARG B:162	BINDING SITE FOR RESIDUE SO4 B 345
16	BC7	SOFTWARE	LYS B:53 , ARG B:56 , LYS B:273 , HOH B:467	BINDING SITE FOR RESIDUE SO4 B 346

(no "SS Bond" information available for 3U0S)

Asymmetric Unit

No.	Residues
1	Ala A:153	-	Pro A:154
2	Ala B:153	-	Pro B:154

(no "SAP(SNP)/Variant" information available for 3U0S)

(no "PROSITE Motif" information available for 3U0S)

(no "Exon" information available for 3U0S)

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:327
 aligned with DFPA_LOLVU | Q7SIG4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:327
                                                              36            37                                                                                                                                                                                                                                                                                     
                                    10        20        30     |   -        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       
           DFPA_LOLVU     1 MEIPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAP-------------EVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee......eeeee.....eeeeehhhhhhhh..hhhhhhhhhh....eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u0s A   1 MEIPVIEPLFTKVTEDIPGATGPVFDKNGDFYIVASPLSEALTKANSPAEAYKASRGAGEILRIDLKTGKKTVICKPEVNGYGGSPIGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCAYCAFDYEGNLWITAPAGEVAPADFTISLREKFGSIYCFTTDGQMIQVDTAFQCPAGIAVRHMNDGRPYQLIVAEQPTKKLWSYDIKGPAKIENKKVWGHIPGTHKGGAAGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPANLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with DFPA_LOLVU | Q7SIG4 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:327
                                                              36            37                                                                                                                                                                                                                                                                                     
                                    10        20        30     |   -        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       
           DFPA_LOLVU     1 MEIPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAP-------------EVEVNGKPAGEILRIDLKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKFGSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWSYDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 314
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee......eeeee.....eeeeehhhhhhhh..hhhhhhhhhh....eeeee......eeeee..ee..ee..eeeeee.....eeeeee...eeeeee....eee................eee.....eeeee..................eeeeee.....eeeeeeee..eeeeeeee.....eeeeeeee....eeeeeeeee..eeeeeeeeee.......eeeeeee.....eeeeee...eeeee........eeee.....eeeeee.....eeeeee....eeeeee.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u0s B   1 MEIPVIEPLFTKVTEDIPGATGPVFDKNGDFYIVASPLSEALTKANSPAEAYKASRGAGEILRIDLKTGKKTVICKPEVNGYGGSPIGCQCDRDANQLFVADMRLGLLVVQTDGTFEEIAKKDSEGRRMQGCAYCAFDYEGNLWITAPAGEVAPADFTISLREKFGSIYCFTTDGQMIQVDTAFQCPAGIAVRHMNDGRPYQLIVAEQPTKKLWSYDIKGPAKIENKKVWGHIPGTHKGGAAGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEKPANLHFKPQTKTIFVTEHENNAVWKFEWQRNGKKQYCETLKFGIF 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

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 3U0S)

(no "CATH Domain" information available for 3U0S)

(no "Pfam Domain" information available for 3U0S)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DFPA_LOLVU | Q7SIG4)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0047862	diisopropyl-fluorophosphatase activity	Catalysis of the reaction: diisopropyl fluorophosphate + H(2)O = diisopropyl phosphate + 2 H(+) + hydrogen fluoride.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

Asymmetric 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
		EPE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:153 - Pro A:154	[ RasMol ]
		Ala B:153 - Pro B:154	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	3u0s
		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
	DFPA_LOLVU \| Q7SIG4
		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)
	3.1.8.2
		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
	DFPA_LOLVU \| Q7SIG4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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