4X00 - JenaLib

Title :   X-RAY CRYSTAL STRUCTURE OF A PUTATIVE ARYL ESTERASE FROM BURKHOLDERIA CENOCEPACIA

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   20 Nov 14 (Deposition) - 03 Dec 14 (Release) - 03 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.38

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 :   Hydrolase, Aryl Esterase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Fairman, T. E. Edwards, D. Lorimer
X-Ray Crystal Structure Of A Putative Aryl Esterase From Burkholderia Cenocepacia
To Be Published
PubMed: search

Compounds

Molecule 1 - PUTATIVE HYDROLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 28-302
	Gene	:	BCAL2527
	Organism Scientific	:	BURKHOLDERIA CENOCEPACIA
	Organism Taxid	:	216591
	Strain	:	ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610

Structural Features

Chains, Units

		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)

Ligands, Modified Residues, Ions (3, 20)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
2	F	3	Ligand/Ion	FLUORIDE ION
3	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	F	-1	Ligand/Ion	FLUORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	F	-1	Ligand/Ion	FLUORIDE ION
3	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	F	-1	Ligand/Ion	FLUORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	F	-1	Ligand/Ion	FLUORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:187 , HOH A:415 , HOH A:438 , HOH A:744 , ARG D:170 , ARG D:174	binding site for residue EDO A 301
02	AC2	SOFTWARE	LEU A:48 , SER A:51 , LEU A:263 , HOH A:662 , HOH A:756	binding site for residue EDO A 302
03	AC3	SOFTWARE	ALA A:228 , ASP A:230 , VAL A:233 , LYS A:234 , ALA A:235 , HOH A:525 , HOH A:617	binding site for residue EDO A 303
04	AC4	SOFTWARE	GLU A:252 , ARG A:268 , ARG A:271 , ASP A:272 , HOH A:421 , GLU D:99	binding site for residue EDO A 304
05	AC5	SOFTWARE	HOH A:406 , HOH A:411 , ILE D:98 , GLU D:99 , TYR D:121 , TYR D:125	binding site for residue EDO A 305
06	AC6	SOFTWARE	ASP A:275 , ARG A:278 , HOH A:417 , HOH A:428 , PRO D:19 , ASP D:20	binding site for residue EDO A 306
07	AC7	SOFTWARE	LYS A:52 , ARG A:179 , PRO A:181 , LEU A:263 , HOH A:566	binding site for residue EDO A 307
08	AC8	SOFTWARE	SER A:112 , LEU A:232	binding site for residue GOL A 308
09	AC9	SOFTWARE	ALA B:228 , ASP B:230 , VAL B:233 , LYS B:234 , ALA B:235 , HOH B:508 , HOH B:585 , HOH B:591	binding site for residue EDO B 301
10	AD1	SOFTWARE	LYS B:77 , ALA B:194 , LEU B:195 , ALA B:196 , LEU C:195	binding site for residue EDO B 302
11	AD2	SOFTWARE	ILE B:98 , GLU B:99 , TYR B:121 , TYR B:125 , HOH B:404 , ARG C:268 , HOH C:415	binding site for residue EDO B 303
12	AD3	SOFTWARE	SER C:187	binding site for residue F B 304
13	AD4	SOFTWARE	ALA C:228 , ASP C:230 , VAL C:233 , LYS C:234 , ALA C:235 , HOH C:517 , HOH C:581	binding site for residue EDO C 301
14	AD5	SOFTWARE	GLU B:99 , GLU C:252 , TYR C:254 , ARG C:268 , ARG C:271 , ASP C:272 , HOH C:404	binding site for residue EDO C 302
15	AD6	SOFTWARE	HIS C:150 , PRO C:151 , GLU C:152 , VAL C:153 , HOH C:695	binding site for residue GOL C 303
16	AD7	SOFTWARE	SER B:187 , ARG C:174	binding site for residue F C 304
17	AD8	SOFTWARE	LEU D:48 , ASN D:49 , SER D:51 , LEU D:188 , LEU D:263 , HOH D:564	binding site for residue EDO D 301
18	AD9	SOFTWARE	TYR A:254 , ALA A:255 , ASP A:256 , GLU A:265 , ARG A:268 , ILE D:98 , GLU D:99 , HOH D:402 , HOH D:441	binding site for residue EDO D 302
19	AE1	SOFTWARE	SER D:112 , TYR D:154 , HOH D:600	binding site for residue GOL D 303
20	AE2	SOFTWARE	SER D:187	binding site for residue F D 304

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

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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeeee.....eeeee.....hhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh.....eeeee.............hhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhh....eeeeee......hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x00 A  11 ARDYTVTAPDGVVLAVQEAGDPEGSPIIFIHGLLGSRLNWSKQLQDPRLQHYRLITYDLRGHGLSGKPAEASSYTDGRRWADDLAAIIESTHARKPVLVGWSLGGAVISNYLAAYGDKGIAGAVYVDGVIELKPDQIVAHPEVYRDMIASDLQTHLDGERAFLRLCFHRQPDATTFSLLLANAALASWDMQRAVRSMTVEAAKGLSKAEVPLLLLYGAQDALVKAKPSIARAKSLNPRIRSELYADSGHAPFLEEPERFNRDLSDFVRMALSR 283
                                    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

Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeeee.....eeeee.....hhhhhhhhhh..hhhh.eeeee.............hhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh.....eeeee.............hhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhh...eeeeee......hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x00 B  12 RDYTVTAPDGVVLAVQEAGDPEGSPIIFIHGLLGSRLNWSKQLQDPRLQHYRLITYDLRGHGLSGKPAEASSYTDGRRWADDLAAIIESTHARKPVLVGWSLGGAVISNYLAAYGDKGIAGAVYVDGVIELKPDQIVAHPEVYRDMIASDLQTHLDGERAFLRLCFHRQPDATTFSLLLANAALASWDMQRAVRSMTVEAAKGLSKAEVPLLLLYGAQDALVKAKPSIARAKSLNPRIRSELYADSGHAPFLEEPERFNRDLSDFVRMALSR 283
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain C from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeeee.....eeeee.....hhhhhhhhhh..hhhh.eeeee.............hhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh.....eeeee.............hhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhh...eeeeee......hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x00 C  11 ARDYTVTAPDGVVLAVQEAGDPEGSPIIFIHGLLGSRLNWSKQLQDPRLQHYRLITYDLRGHGLSGKPAEASSYTDGRRWADDLAAIIESTHARKPVLVGWSLGGAVISNYLAAYGDKGIAGAVYVDGVIELKPDQIVAHPEVYRDMIASDLQTHLDGERAFLRLCFHRQPDATTFSLLLANAALASWDMQRAVRSMTVEAAKGLSKAEVPLLLLYGAQDALVKAKPSIARAKSLNPRIRSELYADSGHAPFLEEPERFNRDLSDFVRMALSR 283
                                    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

Chain D from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeeee.....eeeee.....hhhhhhhhhh..hhhh.eeeee.............hhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh.....eeeee.............hhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhh...eeeeee......hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x00 D  12 RDYTVTAPDGVVLAVQEAGDPEGSPIIFIHGLLGSRLNWSKQLQDPRLQHYRLITYDLRGHGLSGKPAEASSYTDGRRWADDLAAIIESTHARKPVLVGWSLGGAVISNYLAAYGDKGIAGAVYVDGVIELKPDQIVAHPEVYRDMIASDLQTHLDGERAFLRLCFHRQPDATTFSLLLANAALASWDMQRAVRSMTVEAAKGLSKAEVPLLLLYGAQDALVKAKPSIARAKSLNPRIRSELYADSGHAPFLEEPERFNRDLSDFVRMALSR 283
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

Visualization

Interactive Views

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		F	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ 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 ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]
		AD4	[ RasMol ]	+environment [ RasMol ]
		AD5	[ RasMol ]	+environment [ RasMol ]
		AD6	[ RasMol ]	+environment [ RasMol ]
		AD7	[ RasMol ]	+environment [ RasMol ]
		AD8	[ RasMol ]	+environment [ RasMol ]
		AD9	[ RasMol ]	+environment [ RasMol ]
		AE1	[ RasMol ]	+environment [ RasMol ]
		AE2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4x00)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Still Images

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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4x00
		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
	B4E794_BURCJ \| B4E794
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		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

Analysis Tools

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
	B4E794_BURCJ \| B4E794
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description