3QFN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF STREPTOCOCCAL ASYMMETRIC AP4A HYDROLASE AND PHOSPHODIESTERASE SPR1479/SAPH IN COMPLEX WITH INORGANIC PHOSPHATE

Authors :   Y. L. Jiang, J. W. Zhang, W. L. Yu, W. Cheng, C. C. Zhang, C. Z. Zhou, Y. Chen

Date :   22 Jan 11 (Deposition) - 24 Aug 11 (Release) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym./Biol. Unit : A,B

Keywords :   Sandwich Fold, Hydrolase, Fe3+, Mn2+, Po4 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. L. Jiang, J. W. Zhang, W. L. Yu, W. Cheng, C. C. Zhang, C. Frolet, A. -M. Di-Guilmi, T. Vernet, C. Z. Zhou, Y. Chen
Structural And Enzymatic Characterization Of A Streptococca Atp/Diadenosine Polyphosphate And Phosphodiester Hydrolase Spr1479/Saph
To Be Published
PubMed: search

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-262
	Gene	:	SPR1479
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	171101
	Strain	:	R6
	Synonym	:	SAPH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:13 , ASP A:39 , ASN A:66 , TRP A:67 , HIS A:164 , HIS A:166 , MN A:264 , FE A:265 , HOH A:266 , HOH A:292	BINDING SITE FOR RESIDUE PO4 A 263
2	AC2	SOFTWARE	ASP A:39 , ASN A:66 , HIS A:128 , HIS A:164 , PO4 A:263 , FE A:265 , HOH A:266	BINDING SITE FOR RESIDUE MN A 264
3	AC3	SOFTWARE	ASP A:11 , HIS A:13 , ASP A:39 , HIS A:166 , PO4 A:263 , MN A:264 , HOH A:266	BINDING SITE FOR RESIDUE FE A 265
4	AC4	SOFTWARE	HIS B:13 , ASP B:39 , ASN B:66 , TRP B:67 , HIS B:164 , HIS B:166 , MN B:264 , FE B:265 , HOH B:266 , HOH B:278	BINDING SITE FOR RESIDUE PO4 B 263
5	AC5	SOFTWARE	ASP B:39 , ASN B:66 , HIS B:128 , HIS B:164 , PO4 B:263 , FE B:265 , HOH B:266	BINDING SITE FOR RESIDUE MN B 264
6	AC6	SOFTWARE	ASP B:11 , HIS B:13 , ASP B:39 , HIS B:166 , PO4 B:263 , MN B:264 , HOH B:266	BINDING SITE FOR RESIDUE FE B 265

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

Asymmetric/Biological Unit

No.	Residues
1	Met A:42	-	Pro A:43
2	His A:154	-	Pro A:155
3	Met B:42	-	Pro B:43
4	His B:154	-	Pro B:155

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

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

(no "Exon" information available for 3QFN)

Asymmetric/Biological 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:249
 aligned with Q8DNX4_STRR6 | Q8DNX4 from UniProtKB/TrEMBL  Length:282

    Alignment length:249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         
         Q8DNX4_STRR6     3 MTKIALLSDIHGNTTALEAVLADARQLGVDEYWLLGDILMPGTGRRRILDLLDQLPITARVLGNWEDSLWHGVRKELDSTRPSQRYLLRQCQYVLEEISLEEIEVLHNQPLQIHRQFGDLTVGISHHLPDKNWGRELIHTGKQEEFDRLVTHPPCDIAVYGHIHQQLLRYGTGGQLIVNPGSIGQPFFLDAQLRKDLRAQYMILEFDDKGLVDMDFRRVDYDVAAELQLAKDLRLPYFEVYYESLVNGI 251
               SCOP domains d3qfna_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh...eeee..........hhhhhhhhhh..eeee..hhhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeeee..eeeeee................hhhhhhh........eee......eeeee.....eeeee...........hhhhh..eeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qfn A   3 MTKIALLSDIHGNTTALEAVLADARQLGVDEYWLLGDILMPGTGRRRILDLLDQLPITARVLGNWEDSLWHGVRKELDSTRPSQRYLLRQCQYVLEEISLEEIEVLHNQPLQIHRQFGDLTVGISHHLPDKNWGRELIHTGKQEEFDRLVTHPPCDIAVYGHIHQQLLRYGTGGQLIVNPGSIGQPFFLDAQLRKDLRAQYMILEFDDKGLVDMDFRRVDYDVAAELQLAKDLRLPYFEVYYESLVNGI 251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q8DNX4_STRR6 | Q8DNX4 from UniProtKB/TrEMBL  Length:282

    Alignment length:249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         
         Q8DNX4_STRR6     3 MTKIALLSDIHGNTTALEAVLADARQLGVDEYWLLGDILMPGTGRRRILDLLDQLPITARVLGNWEDSLWHGVRKELDSTRPSQRYLLRQCQYVLEEISLEEIEVLHNQPLQIHRQFGDLTVGISHHLPDKNWGRELIHTGKQEEFDRLVTHPPCDIAVYGHIHQQLLRYGTGGQLIVNPGSIGQPFFLDAQLRKDLRAQYMILEFDDKGLVDMDFRRVDYDVAAELQLAKDLRLPYFEVYYESLVNGI 251
               SCOP domains d3qfnb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh...eeee..........hhhhhhhhhh..eeee..hhhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeeee..eeeeee................hhhhhhhhh......eee......eeeee.....eeeee.........hhhhhh...eeeeeeeee..eeeeeeeeee..hhhhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qfn B   3 MTKIALLSDIHGNTTALEAVLADARQLGVDEYWLLGDILMPGTGRRRILDLLDQLPITARVLGNWEDSLWHGVRKELDSTRPSQRYLLRQCQYVLEEISLEEIEVLHNQPLQIHRQFGDLTVGISHHLPDKNWGRELIHTGKQEEFDRLVTHPPCDIAVYGHIHQQLLRYGTGGQLIVNPGSIGQPFFLDAQLRKDLRAQYMILEFDDKGLVDMDFRRVDYDVAAELQLAKDLRLPYFEVYYESLVNGI 251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Metallo-dependent phosphatases (115)

Superfamily: Metallo-dependent phosphatases (115)

Family: automated matches (6)

Protein domain: automated matches (6)

Streptococcus pneumoniae [TaxId: 171101] (3)

1a	d3qfna_	A:
1b	d3qfnb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q8DNX4_STRR6 | Q8DNX4)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.
	GO:0000166		nucleotide binding		Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ 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 ]

	Cis Peptide Bonds
		His A:154 - Pro A:155	[ RasMol ]
		His B:154 - Pro B:155	[ RasMol ]
		Met A:42 - Pro A:43	[ RasMol ]
		Met B:42 - Pro B:43	[ RasMol ]

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	3qfn
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	Q8DNX4_STRR6 \| Q8DNX4	:	3qfm 3qfo

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (2, 2)

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