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Title :   X-RAY CRYSTAL STRUCTURE OF E. COLI YDII COMPLEXED WITH UNDECA-2-ONE-COA

Authors :   W. Ru, J. D. Farelli, D. Dunaway-Mariano, K. N. Allen

Date :   12 Apr 13 (Deposition) - 30 Jul 14 (Release) - 20 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Hotdog Fold, Thioesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Wu, J. A. Latham, D. Chen, J. Farelli, H. Zhao, K. Matthews, K. N. Allen, D. Dunaway-Mariano
Structure And Catalysis In The Escherichia Coli Hotdog-Fold Thioesterase Paralogs Ydii And Ybdb.
Biochemistry V. 53 4788 2014
PubMed-ID: 25010423 | Reference-DOI: 10.1021/BI500334V

Molecule 1 - ESTERASE YDII
	Chains	:	A, B, C, D, E, F, G, H
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1686, JW1676, YDII, YDIL
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 15)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	UOQ	13	Ligand/Ion	UNDECA-2-ONE COENZYME A

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UOQ	4	Ligand/Ion	UNDECA-2-ONE COENZYME A

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UOQ	2	Ligand/Ion	UNDECA-2-ONE COENZYME A

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UOQ	4	Ligand/Ion	UNDECA-2-ONE COENZYME A

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UOQ	3	Ligand/Ion	UNDECA-2-ONE COENZYME A

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:42 , ASP A:43 , SER A:44 , LYS A:47 , GLN A:48 , PRO A:49 , ARG A:94 , GLU A:95 , HOH A:331 , HOH A:390 , HOH A:403 , HOH A:411 , HOH A:416 , ALA B:14 , MET B:15 , GLU B:17 , GLY B:18 , ASN B:19 , PHE E:50 , UOQ E:204 , ILE F:7 , MET F:15 , TYR F:71 , LYS F:79 , VAL F:80	BINDING SITE FOR RESIDUE UOQ A 201
02	AC2	SOFTWARE	TYR A:71 , VAL A:80 , UOQ D:501	BINDING SITE FOR RESIDUE CL A 202
03	AC3	SOFTWARE	GLN A:48 , PRO A:49 , HIS A:54 , GLY A:55 , HIS A:89 , VAL A:90 , ARG A:91 , ARG A:94 , HOH A:399 , HOH A:421 , LEU B:12 , MET B:15 , GLY B:16 , VAL B:21 , PHE B:28 , GLU B:63 , SER B:67 , VAL B:81 , GLY B:82 , LEU B:83 , LEU B:136 , HOH B:343 , HOH B:405 , HIS C:106 , GLY C:108 , SER C:109 , ARG C:110 , HIS C:111	BINDING SITE FOR RESIDUE UOQ A 203
04	AC4	SOFTWARE	HIS B:106 , GLY B:108 , SER B:109 , ARG B:110 , HIS B:111 , HOH B:359 , HOH B:379 , LEU C:12 , MET C:15 , PHE C:28 , GLU C:63 , SER C:67 , VAL C:68 , VAL C:81 , GLY C:82 , LEU C:83 , PRO D:49 , LEU D:53 , HIS D:54 , GLY D:55 , HIS D:89 , VAL D:90 , ARG D:91 , SER D:92	BINDING SITE FOR RESIDUE UOQ B 201
05	AC5	SOFTWARE	LEU A:12 , GLY A:16 , GLU A:63 , SER A:67 , VAL A:81 , GLY A:82 , LEU A:83 , LEU A:136 , GLN B:48 , PRO B:49 , HIS B:54 , GLY B:55 , HIS B:89 , VAL B:90 , ARG B:91 , HOH B:304 , HOH B:391 , HOH B:411 , HIS D:106 , GLY D:108 , SER D:109 , ARG D:110 , HIS D:111 , UOQ D:501	BINDING SITE FOR RESIDUE UOQ B 202
06	AC6	SOFTWARE	HIS A:106 , GLY A:108 , SER A:109 , ARG A:110 , HIS A:111 , GLN C:48 , PRO C:49 , HIS C:54 , GLY C:55 , HIS C:89 , VAL C:90 , ARG C:91 , HOH C:342 , LEU D:12 , GLU D:63 , SER D:67 , VAL D:68 , VAL D:81 , GLY D:82 , HOH D:693 , UOQ H:201	BINDING SITE FOR RESIDUE UOQ C 201
07	AC7	SOFTWARE	VAL A:68 , TYR A:71 , LYS A:79 , VAL A:80 , CL A:202 , PHE B:50 , UOQ B:202 , HOH B:318 , HOH B:354 , HOH B:377 , ALA C:14 , MET C:15 , GLY C:18 , ASN C:19 , HOH C:306 , LYS D:47 , PRO D:49 , HOH D:644 , HOH D:656 , HOH D:685 , HOH D:695 , HOH D:697	BINDING SITE FOR RESIDUE UOQ D 501
08	AC8	SOFTWARE	PHE A:50 , ARG A:94 , ILE B:7 , MET B:15 , TYR B:71 , LYS B:79 , VAL B:80 , HOH B:402 , VAL E:42 , ASP E:43 , SER E:44 , LYS E:47 , GLN E:48 , PRO E:49 , GLU E:95 , GLY E:96 , HOH E:722 , HOH E:726 , HOH E:757 , HOH E:766 , HOH E:776 , ALA F:11 , MET F:15 , GLU F:17 , GLY F:18 , ASN F:19	BINDING SITE FOR RESIDUE UOQ E 201
09	AC9	SOFTWARE	TYR E:71 , VAL E:80 , UOQ H:202	BINDING SITE FOR RESIDUE CL E 202
10	BC1	SOFTWARE	HIS E:106 , GLY E:108 , SER E:109 , ARG E:110 , HIS E:111 , HOH E:763 , HOH E:770 , HOH E:786 , PRO G:49 , HIS G:54 , GLY G:55 , HIS G:89 , VAL G:90 , ARG G:91 , HOH G:248 , LEU H:12 , MET H:15 , PHE H:28 , GLU H:63 , SER H:67 , VAL H:68 , VAL H:81 , GLY H:82	BINDING SITE FOR RESIDUE UOQ E 203
11	BC2	SOFTWARE	UOQ A:201 , GLN E:48 , PRO E:49 , HIS E:54 , GLY E:55 , HIS E:89 , VAL E:90 , ARG E:91 , HOH E:774 , HOH E:781 , LEU F:12 , MET F:15 , PHE F:28 , GLU F:63 , SER F:67 , VAL F:81 , GLY F:82 , LEU F:83 , LEU F:136 , HOH F:370 , HIS G:106 , GLY G:108 , SER G:109 , ARG G:110 , HIS G:111	BINDING SITE FOR RESIDUE UOQ E 204
12	BC3	SOFTWARE	HIS F:106 , GLY F:108 , SER F:109 , ARG F:110 , HIS F:111 , HOH F:378 , MET G:15 , GLU G:63 , VAL G:81 , GLY G:82 , LEU G:83 , GLN H:48 , PRO H:49 , LEU H:53 , HIS H:54 , GLY H:55 , HIS H:89 , VAL H:90 , ARG H:91	BINDING SITE FOR RESIDUE UOQ F 201
13	BC4	SOFTWARE	PHE C:50 , UOQ C:201 , ILE D:7 , MET D:15 , TYR D:71 , LEU D:72 , LYS D:79 , VAL D:80 , ASP G:43 , SER G:44 , LYS G:47 , PRO G:49 , HOH G:221 , ALA H:14 , MET H:15 , GLU H:17 , GLY H:18 , ASN H:19 , HOH H:305 , HOH H:306	BINDING SITE FOR RESIDUE UOQ H 201
14	BC5	SOFTWARE	ARG E:5 , LYS E:6 , ILE E:7 , LEU E:12 , MET E:15 , TYR E:71 , LYS E:79 , CL E:202 , PHE F:50 , HOH F:335 , ALA G:11 , ALA G:14 , MET G:15 , GLU G:17 , GLY G:18 , ASN G:19 , ASP H:43 , SER H:44 , LYS H:47 , PRO H:49 , UOQ H:203 , HOH H:385 , HOH H:428	BINDING SITE FOR RESIDUE UOQ H 202
15	BC6	SOFTWARE	LEU E:12 , GLU E:63 , SER E:67 , VAL E:68 , VAL E:81 , GLY E:82 , LEU E:83 , LEU E:136 , GLN F:48 , PRO F:49 , HIS F:54 , GLY F:55 , HIS F:89 , VAL F:90 , ARG F:91 , HOH F:344 , HIS H:106 , GLY H:108 , SER H:109 , ARG H:110 , HIS H:111 , UOQ H:202 , HOH H:301 , HOH H:372 , HOH H:424 , HOH H:427	BINDING SITE FOR RESIDUE UOQ H 203

(no "SS Bond" information available for 4K4B)

(no "Cis Peptide Bond" information available for 4K4B)

(no "SAP(SNP)/Variant" information available for 4K4B)

(no "PROSITE Motif" information available for 4K4B)

(no "Exon" information available for 4K4B)

Asymmetric Unit

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	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:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh.hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b A   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
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Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b B   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b C   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b D   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain E from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b E   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain F from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b F   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain G from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b G   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain H from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4b H   1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4K4B)

(no "CATH Domain" information available for 4K4B)

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	MENI_ECOLI \| P77781	:	1sbk 1vh5 1vi8 4k49 4k4a

1sbk	ECOLI YDII APO STRUCTURE
4k49
4k4a
4k4c
4k4d

Description

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Ligands, Modified Residues, Ions (2, 15)

Sites (15, 15)

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