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Description

Title :   X-RAY STRUCTURE OF THE PROTEIN Q6F7I0 FROM ACINETOBACTER CALCOACETICUS AMMS 248. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ASR73.

Authors :   A. P. Kuzin, M. Su, S. Jayaraman, D. Wang, H. Janjua, K. Cunningham, L- C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   28 Jun 07 (Deposition) - 17 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   X-Ray, Nesg, Asr73, Acinetobacter Calcoaceticus, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Kuzin, M. Su, S. Jayaraman, D. Wang, H. Janjua, K. Cunningham, L-C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of The Protein Q6F7I0 From Acinetobacter Calcoaceticus Amms 248.
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - 16S RRNA-PROCESSING PROTEIN RIMM
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RIMM, ACIAD3312
	Mutation	:	YES
	Organism Scientific	:	ACINETOBACTER CALCOACETICUS
	Organism Taxid	:	471
	Strain	:	ADP1, AMMS 248

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 6)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:146 , SER A:149 , ASP A:151	BINDING SITE FOR RESIDUE K A 201
2	AC2	SOFTWARE	TYR A:105 , TRP A:106 , GLU A:131 , LEU A:132 , GLU A:134	BINDING SITE FOR RESIDUE UNL A 202

SS Bonds (0, 0)

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

Cis Peptide Bonds (2, 2)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:34	-	Pro A:35
2	Leu A:43	-	Pro A:44

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

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

Exons (0, 0)

(no "Exon" information available for 2QGG)

Sequences/Alignments

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:176
 aligned with RIMM_ACIAD | Q6F7I0 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      
           RIMM_ACIAD     6 NVPEDRIQIGQLRSAYGLNGWLWVYSNTEPMSNMFDYLPWFIETKAGWQTVDVKRWKPHGKGLVVSLKNVSDRNAAESLIGSTIWVAKSQLPKTDVDEYYWSDLKGLTVLGLDEEEQEVNLGQIHELFETGANDVMVVRATADSVDAEERMIPWHKDVVQRVDLEAGRIYVNWGVD 181
               SCOP domains d2qgga1 A:6-103 automated matches                                                                 d2qgga2 A:104-181 automated matches                                            SCOP domains
               CATH domains 2qggA01 A:6-98 RimM N-terminal domain-like                                                   2qggA02 A:99-181 PRC-barrel domain                                                  CATH domains
               Pfam domains -------RimM-2qggA02 A:13-95                                                               -----PRC-2qggA01 A:101-179                                                          -- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeee...hhhhhhhh..eeeee..eeeee.eeeeeee..eeeeee....hhhhhhh....eeeee......hhhhhhhhhhhh..eeeee.....eeeeeeeeeeee....eeeeee..........eeee.....eeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qgg A   6 NVPEDRIQIGQLRSAYGLNGWLWVYSNTEPmSNmFDYLPWYIETKAGWQTVDVKRWKPHGKGLVVSLKGVSDRTGAESLVASNIWIAKSQLPKADVDEYYWSDLKGLTVLGLDDEEQEVNLGQIHELFETGANDVmVVRATPDSIDSEERmIPWHKDVVQRVDLEAGRIYVNWGVD 181
                                    15        25        35|  |    45        55        65        75        85        95       105       115       125       135     | 145       155|      165       175      
                                                         36-MSE                                                                                                  141-MSE        156-MSE                     
                                                            39-MSE

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PRC-barrel domain (113)

Superfamily: PRC-barrel domain (113)

Family: automated matches (2)

Protein domain: automated matches (2)

Acinetobacter calcoaceticus [TaxId: 471] (1)

d2qgga2

A:104-181

Fold: Reductase/isomerase/elongation factor common domain (381)

Superfamily: Translation proteins (218)

Family: automated matches (26)

Protein domain: automated matches (26)

Acinetobacter calcoaceticus [TaxId: 471] (1)

d2qgga1

A:6-103

CATH Domains (2, 2)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Elongation Factor Tu (Ef-tu); domain 3 (323)

Homologous Superfamily: RimM N-terminal domain-like (2)

Acinetobacter calcoaceticus. Organism_taxid: 471. Strain: adp1, amms 248. (1)

2qggA01

A:6-98

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: PRC-barrel domain (3)

Acinetobacter calcoaceticus. Organism_taxid: 471. Strain: adp1, amms 248. (1)

2qggA02

A:99-181

Pfam Domains (2, 2)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PRC-barrel (43)

Family: PRC (42)

Acinetobacter sp. (strain ADP1) (1)

PRC-2qggA01

A:101-179

Clan: no clan defined [family: RimM] (1)

Family: RimM (1)

Acinetobacter sp. (strain ADP1) (1)

RimM-2qggA02

A:13-95

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RIMM_ACIAD | Q6F7I0)

molecular function
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
biological process
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0042274	ribosomal small subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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	Cis Peptide Bonds
		Glu A:34 - Pro A:35	[ RasMol ]
		Leu A:43 - Pro A:44	[ RasMol ]

Still Images

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	2qgg
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (6, 6)

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Related Entries

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