1S3M - JenaLib

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Title :   STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A NOVEL ARCHAEAL PHOSPHODIESTERASE

Authors :   S. Chen, D. Busso, A. F. Yakunin, E. Kuznetsova, M. Proudfoot, J. Jancrick, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   13 Jan 04 (Deposition) - 10 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Phosphodiesterase/Nuclease, Di-Metal-Binding, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chen, A. F. Yakunin, E. Kuznetsova, D. Busso, R. Pufan, M. Proudfoot, R. Kim, S. -H. Kim
Structural And Functional Characterization Of A Novel Phosphodiesterase From Methanococcus Jannaschii
J. Biol. Chem. V. 279 31854 2004
PubMed-ID: 15128743 | Reference-DOI: 10.1074/JBC.M401059200
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN MJ0936
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSKB3
	Expression System Strain	:	BL21/DE3/PSJS1244
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ0936
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NI	4	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:236 , ASN B:259 , HIS B:297 , HIS B:320 , NI B:502 , HOH B:646	BINDING SITE FOR RESIDUE NI B 501
2	AC2	SOFTWARE	ASP B:208 , HIS B:210 , ASP B:236 , HIS B:322 , NI B:501 , HOH B:646	BINDING SITE FOR RESIDUE NI B 502
3	AC3	SOFTWARE	ASP A:8 , ASP A:36 , ASN A:59 , HIS A:97 , HIS A:120 , NI A:504 , HOH A:647	BINDING SITE FOR RESIDUE NI A 503
4	AC4	SOFTWARE	ASP A:8 , HIS A:10 , ASP A:36 , HIS A:122 , NI A:503 , HOH A:647	BINDING SITE FOR RESIDUE NI A 504

(no "SS Bond" information available for 1S3M)

(no "Cis Peptide Bond" information available for 1S3M)

(no "SAP(SNP)/Variant" information available for 1S3M)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0025	PS01269	Uncharacterized protein family UPF0025 signature.	P936_METJA	114-138	2	A:114-138 B:314-338

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0025	PS01269	Uncharacterized protein family UPF0025 signature.	P936_METJA	114-138	1	A:114-138 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0025	PS01269	Uncharacterized protein family UPF0025 signature.	P936_METJA	114-138	1	- B:314-338

(no "Exon" information available for 1S3M)

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
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Chain A from PDB  Type:PROTEIN  Length:165
 aligned with P936_METJA | Q58346 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
           P936_METJA     1 MKIGIMSDTHDHLPNIRKAIEIFNDENVETVIHCGDFVSLFVIKEFENLNANIIATYGNNDGERCKLKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL 165
               SCOP domains d1s3ma_ A: Putative phosphodiesterase MJ0936                                                                                                                          SCOP domains
               CATH domains 1s3mA00 A:1-165  [code=3.60.21.10, no name defined]                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh....eeee......hhhhhhhhhh..eeeee......hhhhhhhhhhhhh...eee.eeeeee..eeeeee...hhhhhhhhhhhh...eee.......eeeee..eeeee............eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------UPF0025  PDB: A:114-138  --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s3m A   1 MKIGIMSDTHDHLPNIRKAIEIFNDENVETVIHCGDFVSLFVIKEFENLNANIIATYGNNDGERCKLKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with P936_METJA | Q58346 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
           P936_METJA     1 MKIGIMSDTHDHLPNIRKAIEIFNDENVETVIHCGDFVSLFVIKEFENLNANIIATYGNNDGERCKLKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL 165
               SCOP domains d1s3mb_ B: Putative phosphodiesterase MJ0936                                                                                                                          SCOP domains
               CATH domains 1s3mB00 B:201-365  [code=3.60.21.10, no name defined]                                                                                                                 CATH domains
           Pfam domains (1) Metallophos-1s3mB01 B:201-324                                                                                               ----------------------------------------- Pfam domains (1)
           Pfam domains (2) Metallophos-1s3mB02 B:201-324                                                                                               ----------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh....eeee......hhhhhhhhhh..eeeee......hhhhhhhhhhhhh...eee.eeeeee..eeeeee...hhhhhhhhhhhh...eee.......eeeee..eeeee............eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------UPF0025  PDB: B:314-338  --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s3m B 201 MKIGIMSDTHDHLPNIRKAIEIFNDENVETVIHCGDFVSLFVIKEFENLNANIIATYGNNDGERCKLKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQSVLEMAIKSGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIPTIGILDTEKKEYREIVL 365
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 Unit

Classes(

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

Fold: Metallo-dependent phosphatases (115)

Superfamily: Metallo-dependent phosphatases (115)

Family: YfcE-like (12)

Protein domain: Putative phosphodiesterase MJ0936 (3)

Methanococcus jannaschii [TaxId: 2190] (3)

1a	d1s3ma_	A:
1b	d1s3mb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Purple Acid Phosphatase; chain A, domain 2 (87)

Homologous Superfamily: [code=3.60.21.10, no name defined] (83)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

1a	1s3mA00	A:1-165
1b	1s3mB00	B:201-365

Asymmetric Unit(hide GO term definitions)

Chain A,B (P936_METJA | Q58346)

molecular function
	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:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

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