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Title :   CRYSTAL STRUCTURE OF DEOXYRIBONUCLEOTIDASE-LIKE PROTEIN (NP_764060.1) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 1.55 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   10 Jan 08 (Deposition) - 22 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Np_764060. 1, Deoxyribonucleotidase-Like Protein, 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 Deoxyribonucleotidase-Like Protein (Np_764060. 1) From Staphylococcus Epidermidis Atcc 12228 At 1. 55 A Resolution
To Be Published
PubMed: search

Molecule 1 - PUTATIVE 5'(3')-DEOXYRIBONUCLEOTIDASE
	Chains	:	A, B
	EC Number	:	3.1.3.-
	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_764060.1, SE_0505
	Organism Scientific	:	STAPHYLOCOCCUS EPIDERMIDIS
	Organism Taxid	:	176280
	Strain	:	ATCC 12228

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:9 , ASP A:11 , ASP A:135 , HOH A:374 , HOH A:378 , HOH A:384	BINDING SITE FOR RESIDUE MG A 300
2	AC2	SOFTWARE	ASP B:9 , ASP B:11 , ASP B:135 , HOH B:383 , HOH B:386 , HOH B:387	BINDING SITE FOR RESIDUE MG B 300

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

(no "Cis Peptide Bond" information available for 3BWV)

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

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

(no "Exon" information available for 3BWV)

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
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Chain A from PDB  Type:PROTEIN  Length:167
 aligned with 53DR_STAES | Q8CTG7 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
           53DR_STAES     2 TRQRIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMIPEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQLNEHYDIYIATAAMDVPTSFHDKYEWLLEYFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVYEHRFERVSGWRDVKNYFNSIE 178
               SCOP domains d3bwva_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains 3bwvA01        3bwvA02 A:17-65 Deoxyribonu        cleotidase; do3bwvA01 A:2-16,A:66-178  [c  ode=3.40.50.1000, no name defined]                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhh....hhhhh.....--------hhhhhhhhh.hhhhh.....hhhhhhhhhh...eeeeee..--..hhhhhhhhhhhhhh...hhh.eee..hhhhh...eeee.hhhhhhhh..eeeee.hhhhh.....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwv A   2 TRQRIAIDmDEVLADTLGAVVKAVNERADLNIKmESLNGKKL--------GLVmDILKEPGFFRNLDVmPHAQEVVKQLNEHYDIYIATAA--VPTSFHDKYEWLLEYFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSImFTASHNVYEHRFERVSGWRDVKNYFNSIE 178
                                    11        21        31   |    41 |       -|  |    61        71        81        91|  |   101       111       121       131       141       151       161       171       
                                   10-MSE                   35-MSE  43       52  |             70-MSE                92 95                                                   149-MSE                         
                                                                                55-MSE

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with 53DR_STAES | Q8CTG7 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      
           53DR_STAES     3 RQRIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMIPEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQLNEHYDIYIATAAMDVPTSFHDKYEWLLEYFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVYEHRFERVSGWRDVKNYFNSIE 178
               SCOP domains d3bwvb_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains 3bwvB01       3bwvB02 B:17-65 Deoxyribonu        cleotidase; do3bwvB01 B:3-16,B:66-178  [code=3.40.50.1000, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhh....hhhhhh....--------hhhhhhhhh...........hhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...hhh.eee..hhhhh...eeee.hhhhhh....eeeee.hhhhh.....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwv B   3 RQRIAIDmDEVLADTLGAVVKAVNERADLNIKmESLNGKKL--------GLVmDILKEPGFFRNLDVmPHAQEVVKQLNEHYDIYIATAAmDVPTSFHDKYEWLLEYFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSImFTASHNVYEHRFERVSGWRDVKNYFNSIE 178
                                   |12        22        32  |     42|       52  |     62       |72        82        92|      102       112       122       132       142      |152       162       172      
                                  10-MSE                   35-MSE  43       52  |             70-MSE                 93-MSE                                                 149-MSE                         
                                                                               55-MSE

Legend:		→ Mismatch	(orange background)
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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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: automated matches (99)

Protein domain: automated matches (99)

Staphylococcus epidermidis [TaxId: 176280] (1)

1a	d3bwva_	A:
1b	d3bwvb_	B:

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (53DR_STAES | Q8CTG7)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
	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.
biological process
	GO:0009264	deoxyribonucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (3, 15)

Sites (2, 2)

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