3P96 - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE SERB FROM MYCOBACTERIUM AVIUM, NATIVE FORM

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   15 Oct 10 (Deposition) - 10 Nov 10 (Release) - 11 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Ssgcid, Phosphoserine Phosphatase Serb, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Abendroth, A. S. Gardberg, J. I. Robinson, J. S. Christensen, B. L. Staker, P. J. Myler, L. J. Stewart, T. E. Edwards
Sad Phasing Using Iodide Ions In A High-Throughput Structural Genomics Environment.
J. Struct. Funct. Genom. V. 12 83 2011
PubMed-ID: 21359836 | Reference-DOI: 10.1007/S10969-011-9101-7
(for further references see the PDB file header)

Molecule 1 - PHOSPHOSERINE PHOSPHATASE SERB
	Chains	:	A
	EC Number	:	3.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SERB, MAV_3907
	Organism Scientific	:	MYCOBACTERIUM AVIUM
	Organism Taxid	:	243243
	Strain	:	104

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:187 , ASP A:189 , ASP A:343 , HOH A:429 , HOH A:440 , HOH A:451	BINDING SITE FOR RESIDUE MG A 412
2	AC2	SOFTWARE	ASP A:187 , GLY A:276 , LYS A:320 , ASN A:346 , HOH A:440 , HOH A:461	BINDING SITE FOR RESIDUE CL A 413
3	AC3	SOFTWARE	ASP A:189 , ARG A:232 , GLY A:277 , HOH A:502	BINDING SITE FOR RESIDUE EDO A 414

(no "SS Bond" information available for 3P96)

Asymmetric Unit

No.	Residues
1	Arg A:105	-	Pro A:106
2	Tyr A:135	-	Pro A:136
3	Gly A:312	-	Pro A:313

(no "SAP(SNP)/Variant" information available for 3P96)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	SERB_MYCA1	10-88	1	A:10-88

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	SERB_MYCA1	10-88	2	A:10-88

(no "Exon" information available for 3P96)

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:396
 aligned with SERB_MYCA1 | A0QJI1 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:396
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394      
           SERB_MYCA1     5 PKVSVLITVTGVDQPGVTATLFEVLSGHGVELLNVEQVVIRHRLTLGVLVCCPADVADGPALRHDVEAAIRKVGLDVSIERSDDVPIIREPSTHTIFVLGRPITAAAFGAVAREVAALGVNIDLIRGVSDYPVIGLELRVSVPPGADGALRTALNRVSSEEHVDVAVEDYTLERRAKRLIVFDVDSTLVQGEVIEMLAAKAGAEGQVAAITDAAMRGELDFAQSLQQRVATLAGLPATVIDEVAGQLELMPGARTTLRTLRRLGYACGVVSGGFRRIIEPLAEELMLDYVAANELEIVDGTLTGRVVGPIIDRAGKATALREFAQRAGVPMAQTVAVGDGANDIDMLAAAGLGIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIEAADAID 400
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---ACT_6-3p96A01 A:8-84                                                         ---------------------------------------------------------------------------------------------------HAD-3p96A02 A:184-352                                                                                                                                                    ------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee...hhhhhhhhhhh....eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeee............eeeeeee...hhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhh.eeeeee.........eeee.........hhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh...eeeee.eeee..eeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhhhh.eee.....hhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----ACT  PDB: A:10-88 UniProt: 10-88                                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p96 A   5 PKVSVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCPADVADGPALRHDVEAAIRKVGLDVSIERSDDVPIIREPSTHTIFVLGRPITAAAFGAVAREVAALGVNIDLIRGVSDYPVIGLELRVSVPPGADEALRTALNRVSSEEHVDVAVEDYTLERRAKRLIVFDVDSTLVQGEVIEMLAAKAGAEGQVAAITDAAMRGELDFAQSLQQRVATLAGLPATVIDEVAGQLELMPGARTTLRTLRRLGYACGVVSGGFRRIIEPLAEELMLDYVAANELEIVDGTLTGRVVGPIIDRAGKATALREFAQRAGVPMAQTVAVGDGANDIDMLAAAGLGIAFNAKPALREVADASLSHPYLDTVLFLLGVTRGEIEAADAID 400
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394

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 3P96)

(no "CATH Domain" information available for 3P96)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ACT (34)

Family: ACT_6 (3)

Mycobacterium avium (strain 104) (1)

ACT_6-3p96A01

A:8-84

Clan: HAD (186)

Family: HAD (3)

Mycobacterium avium (strain 104) (1)

HAD-3p96A02

A:184-352

Asymmetric Unit(hide GO term definitions)

Chain A (SERB_MYCA1 | A0QJI1)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004647	phosphoserine phosphatase activity	Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
biological process
	GO:0006564	L-serine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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	Cis Peptide Bonds
		Arg A:105 - Pro A:106	[ RasMol ]
		Gly A:312 - Pro A:313	[ RasMol ]
		Tyr A:135 - Pro A:136	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	3p96
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	SERB_MYCA1 \| A0QJI1	:	5is2 5it0 5it4 5jjb 5jlp 5jlr 5jma 5t41

(no "Related Entries Specified in the PDB File" available for 3P96)

Description

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Ligands, Modified Residues, Ions (3, 3)

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SS Bonds (0, 0)

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