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Title :   CRYSTAL STRUCTURE OF A PUTATIVE ENDORIBONUCLEASE (SO_1960) FROM SHEWANELLA ONEIDENSIS MR-1 AT 1.85 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   08 Feb 07 (Deposition) - 20 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Np_717567. 1) Fro Shewanella Oneidensis At 1. 85 A Resolution
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN
	Chains	:	A, B, C
	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_717567.1, SO_1960
	Organism Scientific	:	SHEWANELLA ONEIDENSIS
	Organism Taxid	:	211586
	Strain	:	MR-1

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 23)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	CA	1	Ligand/Ion	CALCIUM ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
5	NA	3	Ligand/Ion	SODIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:186 , HOH A:191 , HOH B:191 , HOH B:192 , HOH B:242 , HOH C:168 , HOH C:209	BINDING SITE FOR RESIDUE CA A 154
02	AC2	SOFTWARE	ASP A:58 , HOH A:168 , HOH A:181 , HOH A:195 , HOH A:307 , GLU B:63 , NA B:154	BINDING SITE FOR RESIDUE NA A 155
03	AC3	SOFTWARE	ASP C:58 , GLU C:63 , HOH C:170 , HOH C:184 , HOH C:193	BINDING SITE FOR RESIDUE NA C 154
04	AC4	SOFTWARE	GLU A:63 , NA A:155 , HOH A:168 , HOH A:181 , ASP B:58 , HOH B:182	BINDING SITE FOR RESIDUE NA B 154
05	AC5	SOFTWARE	TYR B:26 , PRO C:109 , ARG C:131 , ILE C:133 , HOH C:157	BINDING SITE FOR RESIDUE ACT C 155
06	AC6	SOFTWARE	PRO A:109 , ARG A:131 , ILE A:133 , HOH A:170 , TYR C:26	BINDING SITE FOR RESIDUE ACT A 156
07	AC7	SOFTWARE	TYR A:26 , PRO B:109 , ARG B:131 , HOH B:159	BINDING SITE FOR RESIDUE ACT B 155
08	AC8	SOFTWARE	GLY B:24 , ASN B:25 , HOH B:278 , ASP C:113	BINDING SITE FOR RESIDUE ACT B 156
09	AC9	SOFTWARE	GLN A:52 , LEU A:141 , ILE B:106	BINDING SITE FOR RESIDUE ACT A 157
10	BC1	SOFTWARE	GLU B:6 , LEU B:14 , GLU B:15 , LEU B:16 , HOH B:300	BINDING SITE FOR RESIDUE GOL B 157

(no "SS Bond" information available for 2OTM)

(no "Cis Peptide Bond" information available for 2OTM)

(no "SAP(SNP)/Variant" information available for 2OTM)

(no "PROSITE Motif" information available for 2OTM)

(no "Exon" information available for 2OTM)

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:152
 aligned with Q8EFL1_SHEON | Q8EFL1 from UniProtKB/TrEMBL  Length:153

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
         Q8EFL1_SHEON     2 MNTPESRLVAAGLELPEVAAALGNYEPYSIVGSQLMTSGQFPYLQGKLLYQGQLGADYTVSEGYAACRLATLNAIAQLKQACGELSRIKQIYRLEGVLNVHQSCIEHPKALDGASDLLLEIFGEAGRHSRMIWTNPVMPLNSLCLVYLFAEL 153
               SCOP domains d2otma1 A:2-153 Hypothetical protein SO1960                                                                                                              SCOP domains
               CATH domains -2otmA00 A:3-153  [code=3.30.1330.40, no name defined]                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh................eeee..eeee.....ee..ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otm A   2 mNTPESRLVAAGLELPEVAAALGNYEPYSIVGSQLmTSGQFPYLQGKLLYQGQLGADYTVSEGYAACRLATLNAIAQLKQACGELSRIKQIYRLEGVLNVHQSCIEHPKALDGASDLLLEIFGEAGRHSRmIWTNPVmPLNSLCLVYLFAEL 153
                            |       11        21        31     |  41        51        61        71        81        91       101       111       121       131|      141       151  
                            |                                 37-MSE                                                                                        132-MSE  |              
                            2-MSE                                                                                                                                  139-MSE

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with Q8EFL1_SHEON | Q8EFL1 from UniProtKB/TrEMBL  Length:153

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
         Q8EFL1_SHEON     1 MMNTPESRLVAAGLELPEVAAALGNYEPYSIVGSQLMTSGQFPYLQGKLLYQGQLGADYTVSEGYAACRLATLNAIAQLKQACGELSRIKQIYRLEGVLNVHQSCIEHPKALDGASDLLLEIFGEAGRHSRMIWTNPVMPLNSLCLVYLFAEL 153
               SCOP domains d2otmb_ B: Hypothetical protein SO1960                                                                                                                    SCOP domains
               CATH domains --2otmB00 B:3-153  [code=3.30.1330.40, no name defined]                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh................eeee..eeee.....ee..ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otm B   1 mmNTPESRLVAAGLELPEVAAALGNYEPYSIVGSQLmTSGQFPYLQGKLLYQGQLGADYTVSEGYAACRLATLNAIAQLKQACGELSRIKQIYRLEGVLNVHQSCIEHPKALDGASDLLLEIFGEAGRHSRmIWTNPVmPLNSLCLVYLFAEL 153
                            ||      10        20        30      | 40        50        60        70        80        90       100       110       120       130 |     140       150   
                            1-MSE                              37-MSE                                                                                        132-MSE  |              
                             2-MSE                                                                                                                                  139-MSE

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q8EFL1_SHEON | Q8EFL1 from UniProtKB/TrEMBL  Length:153

    Alignment length:151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152 
         Q8EFL1_SHEON     3 NTPESRLVAAGLELPEVAAALGNYEPYSIVGSQLMTSGQFPYLQGKLLYQGQLGADYTVSEGYAACRLATLNAIAQLKQACGELSRIKQIYRLEGVLNVHQSCIEHPKALDGASDLLLEIFGEAGRHSRMIWTNPVMPLNSLCLVYLFAEL 153
               SCOP domains d2otmc_ C: Hypothetical protein SO1960                                                                                                                  SCOP domains
               CATH domains 2otmC00 C:3-153  [code=3.30.1330.40, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh................eeee..eeee.....ee..ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2otm C   3 NTPESRLVAAGLELPEVAAALGNYEPYSIVGSQLmTSGQFPYLQGKLLYQGQLGADYTVSEGYAACRLATLNAIAQLKQACGELSRIKQIYRLEGVLNVHQSCIEHPKALDGASDLLLEIFGEAGRHSRmIWTNPVmPLNSLCLVYLFAEL 153
                                    12        22        32    |   42        52        62        72        82        92       102       112       122       132      |142       152 
                                                             37-MSE                                                                                        132-MSE  |              
                                                                                                                                                                  139-MSE

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	-	→ 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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Bacillus chorismate mutase-like (324)

Superfamily: YjgF-like (45)

Family: YjgF/L-PSP (23)

Protein domain: Hypothetical protein SO1960 (1)

Shewanella oneidensis [TaxId: 70863] (1)

1a	d2otma1	A:2-153
1b	d2otmb_	B:
1c	d2otmc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.40, no name defined] (35)

Shewanella oneidensis mr-1. Organism_taxid: 211586. Strain: mr-1. (1)

1a	2otmA00	A:3-153
1b	2otmB00	B:3-153
1c	2otmC00	C:3-153

(no "Pfam Domain" information available for 2OTM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (Q8EFL1_SHEON | Q8EFL1)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric/Biological Unit
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