3B5Q - JenaLib

Title :   CRYSTAL STRUCTURE OF A PUTATIVE SULFATASE (NP_810509.1) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.40 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   26 Oct 07 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Np_810509. 1, Putative Sulfatase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Sulfatase (Np_810509. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 2. 40 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - PUTATIVE SULFATASE YIDJ
	Atcc	:	29148
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_810509.1, BT_1596
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON VPI-5482
	Organism Taxid	:	226186
	Strain	:	VPI-5482, DSM 2079, NCTC 10582

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (6, 57)

Asymmetric Unit (6, 57)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	25	Ligand/Ion	1,2-ETHANEDIOL
3	EPE	3	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
5	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 26)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
3	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
5	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 27)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
3	EPE	3	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
5	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	ZN	-1	Ligand/Ion	ZINC ION

Sites (35, 35)

Asymmetric Unit (35, 35)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:225 , CYS A:226 , HIS A:462 , HIS A:469	BINDING SITE FOR RESIDUE ZN A 500
02	AC2	SOFTWARE	CYS B:225 , CYS B:226 , HIS B:462 , HIS B:469	BINDING SITE FOR RESIDUE ZN B 500
03	AC3	SOFTWARE	SER A:377 , GLU A:378 , TYR A:379 , GLU A:380 , TYR A:381 , VAL A:382	BINDING SITE FOR RESIDUE CL A 501
04	AC4	SOFTWARE	GLU B:378 , TYR B:379 , GLU B:380 , TYR B:381 , VAL B:382	BINDING SITE FOR RESIDUE CL B 501
05	AC5	SOFTWARE	ARG A:393 , LYS A:411 , GLU B:204 , LEU B:205 , PRO B:206 , ASP B:207 , PHE B:209 , ASP B:210 , ARG B:417	BINDING SITE FOR RESIDUE EPE B 502
06	AC6	SOFTWARE	LYS A:412 , GLU B:212 , ASP B:213 , TRP B:214	BINDING SITE FOR RESIDUE EPE B 503
07	AC7	SOFTWARE	SER B:64 , ASN B:85 , LYS B:117 , HIS B:119 , HIS B:180 , CYS B:183 , ARG B:229 , ARG B:230 , LYS B:296 , GLU B:378 , TYR B:379 , HOH B:547 , HOH B:611	BINDING SITE FOR RESIDUE EPE B 504
08	AC8	SOFTWARE	PHE A:137 , THR A:138 , PHE A:149 , TYR A:268 , HOH A:563 , HOH A:664 , HOH A:691	BINDING SITE FOR RESIDUE EDO A 502
09	AC9	SOFTWARE	LEU A:327 , THR A:328 , ASP A:333 , ILE A:353 , LEU A:355 , SER A:367 , HIS A:368	BINDING SITE FOR RESIDUE EDO A 503
10	BC1	SOFTWARE	GLY A:39 , CYS A:40 , THR A:41 , LEU A:42 , LYS A:258	BINDING SITE FOR RESIDUE EDO A 504
11	BC2	SOFTWARE	LEU B:327 , THR B:328 , ASP B:333 , LEU B:355 , SER B:367 , HIS B:368	BINDING SITE FOR RESIDUE EDO B 505
12	BC3	SOFTWARE	LYS A:412 , ASP B:210 , TRP B:214 , ARG B:292	BINDING SITE FOR RESIDUE EDO A 505
13	BC4	SOFTWARE	SER A:49	BINDING SITE FOR RESIDUE EDO A 506
14	BC5	SOFTWARE	ILE B:217 , PRO B:218 , GLU B:405	BINDING SITE FOR RESIDUE EDO B 506
15	BC6	SOFTWARE	VAL A:211 , GLU A:212 , ASP A:213 , ILE A:217 , ARG A:417 , LYS A:418 , ASN A:419 , HOH A:553	BINDING SITE FOR RESIDUE EDO A 507
16	BC7	SOFTWARE	LEU B:326 , LEU B:327 , SER B:367 , HIS B:368 , EDO B:512	BINDING SITE FOR RESIDUE EDO B 507
17	BC8	SOFTWARE	ARG A:29 , THR A:37 , ILE A:246 , GLN A:250 , MSE A:288	BINDING SITE FOR RESIDUE EDO A 508
18	BC9	SOFTWARE	CYS B:226 , ARG B:458 , CYS B:459 , HIS B:469 , GLU B:470 , GLY B:471 , PRO B:472 , GLY B:473	BINDING SITE FOR RESIDUE EDO B 508
19	CC1	SOFTWARE	PRO A:89 , ASN A:91 , THR A:92 , ARG B:393 , TYR B:394	BINDING SITE FOR RESIDUE EDO A 509
20	CC2	SOFTWARE	ALA A:134 , LYS A:135 , PRO A:136 , ARG A:274 , PRO A:314 , HOH A:596	BINDING SITE FOR RESIDUE EDO A 510
21	CC3	SOFTWARE	ILE A:217 , PRO A:218 , GLY A:404 , GLU A:405 , LYS A:422	BINDING SITE FOR RESIDUE EDO A 511
22	CC4	SOFTWARE	ASP A:139 , PRO A:140 , GLU A:141 , ARG A:196 , LYS A:265	BINDING SITE FOR RESIDUE EDO A 512
23	CC5	SOFTWARE	HIS B:251 , LYS B:254 , LYS B:258	BINDING SITE FOR RESIDUE EDO B 509
24	CC6	SOFTWARE	ASP B:139 , ARG B:196 , LYS B:265 , HOH B:692	BINDING SITE FOR RESIDUE EDO B 510
25	CC7	SOFTWARE	LYS B:128	BINDING SITE FOR RESIDUE EDO B 511
26	CC8	SOFTWARE	ASP B:324 , PRO B:392 , EDO B:507 , EDO B:513	BINDING SITE FOR RESIDUE EDO B 512
27	CC9	SOFTWARE	ARG B:390 , PRO B:392 , EDO B:512	BINDING SITE FOR RESIDUE EDO B 513
28	DC1	SOFTWARE	ARG B:292	BINDING SITE FOR RESIDUE EDO A 513
29	DC2	SOFTWARE	LYS A:365 , ASP B:454 , ASP B:456 , HOH B:694	BINDING SITE FOR RESIDUE EDO B 514
30	DC3	SOFTWARE	GLN A:28 , ARG A:29 , GLN A:36 , HOH A:700	BINDING SITE FOR RESIDUE EDO A 514
31	DC4	SOFTWARE	HIS A:251 , LYS A:254 , LYS A:258	BINDING SITE FOR RESIDUE EDO A 515
32	DC5	SOFTWARE	ALA B:134 , LYS B:135 , ARG B:274 , GLY B:313 , PRO B:314 , HOH B:693	BINDING SITE FOR RESIDUE EDO B 515
33	DC6	SOFTWARE	PRO B:43 , GLU B:46 , ARG B:50 , PHE B:137 , THR B:138 , VAL B:144 , TYR B:268	BINDING SITE FOR RESIDUE PEG B 516
34	DC7	SOFTWARE	LYS B:15 , SER B:108 , TYR B:110 , PRO B:169 , ALA B:342	BINDING SITE FOR RESIDUE PEG B 517
35	DC8	SOFTWARE	LYS A:15 , SER A:108 , PRO A:169 , ALA A:342 , GLY A:343	BINDING SITE FOR RESIDUE PEG A 516

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Asymmetric Unit

No.	Residues
1	Glu A:88	-	Pro A:89
2	Pro A:166	-	Lys A:167
3	Glu A:168	-	Pro A:169
4	Asn A:178	-	Pro A:179
5	Glu A:476	-	Ile A:477
6	Glu B:88	-	Pro B:89
7	Glu B:168	-	Pro B:169
8	Asn B:178	-	Pro B:179

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:464
 aligned with Q8A7C8_BACTN | Q8A7C8 from UniProtKB/TrEMBL  Length:481

    Alignment length:464
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473    
         Q8A7C8_BACTN    14 EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCPLSQPSRAALWSGMMPHQTNVRSNSSEPVNTRLPENVPTLGSLFSESGYEAVHFGKTHDMGSLRGFKHKEPVAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNPPKEPFICIADFQNPHNICGFIGENAGVHTDRPISGPLPELPDNFDVEDWSNIPTPVQYICCSHRRMTQAAHWNEENYRHYIAAFQHYTKMVSKQVDSVLKALYSTPAGRNTIVVIMADHGDGMASHRMVTKHISFYDEMTNVPFIFAGPGIKQQKKPVDHLLTQPTLDLLPTLCDLAGIAVPAEKAGISLAPTLRGEKQKKSHPYVVSEWHSEYEYVTTPGRMVRGPRYKYTHYLEGNGEELYDMKKDPGERKNLAKDPKYSKILAEHRALLDDYITRSKDDYRSLKVDADPRCRNHTPGYPSHEGPGAREI 477
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhh.....hhhhhhhhhh.ee.........hhhhhhhhhhhh.hhhhhh..................hhhhhhhhh..eeeeee...........eee..............hhhhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeee......hhhhh.......hhhhhh..eeee................hhhhhhhhhhhhhhh...........hhhhhh..........eeeeeee.....eeeeeeee...eeeeee....eeeeee.............hhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhh....hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b5q A  14 EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCPLSQPSRAALWSGmmPHQTNVRSNSSEPVNTRLPENVPTLGSLFSESGYEAVHFGKTHDmGSLRGFKHKEPVAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNPPKEPFICIADFQNPHNICGFIGENAGVHTDRPISGPLPELPDNFDVEDWSNIPTPVQYICCSHRRmTQAAHWNEENYRHYIAAFQHYTKmVSKQVDSVLKALYSTPAGRNTIVVImADHGDGmASHRmVTKHISFYDEmTNVPFIFAGPGIKQQKKPVDHLLTQPTLDLLPTLCDLAGIAVPAEKAGISLAPTLRGEKQKKSHPYVVSEWHSEYEYVTTPGRmVRGPRYKYTHYLEGNGEELYDmKKDPGERKNLAKDPKYSKILAEHRALLDDYITRSKDDYRSLKVDADPRCRNHTPGYPSHEGPGAREI 477
                                    23        33        43        53        63        73 ||     83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253 |     263       273       283    |  293       303|      313       323       333       343       353       363       373       383    |  393       403      |413       423       433       443       453       463       473    
                                                                                        75-MSE                                       121-MSE                                                                                                       231-MSE                 255-MSE                   281-MSE  |    |        304-MSE                                                                             388-MSE               410-MSE                                                               
                                                                                         76-MSE                                                                                                                                                                                                             288-MSE|                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                 293-MSE

Chain B from PDB  Type:PROTEIN  Length:467
 aligned with Q8A7C8_BACTN | Q8A7C8 from UniProtKB/TrEMBL  Length:481

    Alignment length:467
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       
         Q8A7C8_BACTN    14 EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCPLSQPSRAALWSGMMPHQTNVRSNSSEPVNTRLPENVPTLGSLFSESGYEAVHFGKTHDMGSLRGFKHKEPVAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNPPKEPFICIADFQNPHNICGFIGENAGVHTDRPISGPLPELPDNFDVEDWSNIPTPVQYICCSHRRMTQAAHWNEENYRHYIAAFQHYTKMVSKQVDSVLKALYSTPAGRNTIVVIMADHGDGMASHRMVTKHISFYDEMTNVPFIFAGPGIKQQKKPVDHLLTQPTLDLLPTLCDLAGIAVPAEKAGISLAPTLRGEKQKKSHPYVVSEWHSEYEYVTTPGRMVRGPRYKYTHYLEGNGEELYDMKKDPGERKNLAKDPKYSKILAEHRALLDDYITRSKDDYRSLKVDADPRCRNHTPGYPSHEGPGAREILKR 480
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhh.....hhhhhhhhhhhee.........hhhhhhhhhhhh.hhhhhh..................hhhhhhhhh..eeeeee...........eee..............hhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeee......hhhhh.......hhhhhh..eeee................hhhhhhhhhhhhhh............hhhhhhh.........eeeee..........eeeee...eeeeee.hhheeeeee.............hhhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhh....hhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b5q B  14 EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCPLSQPSRAALWSGmmPHQTNVRSNSSEPVNTRLPENVPTLGSLFSESGYEAVHFGKTHDmGSLRGFKHKEPVAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNPPKEPFICIADFQNPHNICGFIGENAGVHTDRPISGPLPELPDNFDVEDWSNIPTPVQYICCSHRRmTQAAHWNEENYRHYIAAFQHYTKmVSKQVDSVLKALYSTPAGRNTIVVImADHGDGmASHRmVTKHISFYDEmTNVPFIFAGPGIKQQKKPVDHLLTQPTLDLLPTLCDLAGIAVPAEKAGISLAPTLRGEKQKKSHPYVVSEWHSEYEYVTTPGRmVRGPRYKYTHYLEGNGEELYDmKKDPGERKNLAKDPKYSKILAEHRALLDDYITRSKDDYRSLKVDADPRCRNHTPGYPSHEGPGAREILKR 480
                                    23        33        43        53        63        73 ||     83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253 |     263       273       283    |  293       303|      313       323       333       343       353       363       373       383    |  393       403      |413       423       433       443       453       463       473       
                                                                                        75-MSE                                       121-MSE                                                                                                       231-MSE                 255-MSE                   281-MSE  |    |        304-MSE                                                                             388-MSE               410-MSE                                                                  
                                                                                         76-MSE                                                                                                                                                                                                             288-MSE|                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                 293-MSE

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Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (4, 4)

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	Cis Peptide Bonds
		Asn A:178 - Pro A:179	[ RasMol ]
		Asn B:178 - Pro B:179	[ RasMol ]
		Glu A:168 - Pro A:169	[ RasMol ]
		Glu A:476 - Ile A:477	[ RasMol ]
		Glu A:88 - Pro A:89	[ RasMol ]
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