1RFZ - JenaLib

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Title :   STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION FROM BACILLUS STEAROTHERMOPHILUS

Authors :   Y. Kim, R. Wu, M. E. Cuff, P. Quartey, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   10 Nov 03 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Structural Genomics, Hypothetical Protein, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, R. Wu, M. E. Cuff, P. Quartey, A. Joachimiak
Structure Of Hypothetical Protein Apc35681 From Bacillus Stearothermophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN APC35681
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 16)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	7	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:53 , LYS A:57 , TYR A:108 , ARG A:156	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	ARG B:53 , LYS B:57 , TYR B:108 , ARG B:156	BINDING SITE FOR RESIDUE SO4 B 402
3	AC3	SOFTWARE	ARG C:53 , LYS C:57 , TYR C:108 , ARG C:156	BINDING SITE FOR RESIDUE SO4 C 403
4	AC4	SOFTWARE	ARG D:53 , LYS D:57 , TYR D:108 , ARG D:156 , ARG D:160	BINDING SITE FOR RESIDUE SO4 D 404
5	AC5	SOFTWARE	LYS A:57 , ARG A:58 , HOH A:422 , HOH A:434	BINDING SITE FOR RESIDUE SO4 A 405
6	AC6	SOFTWARE	HIS A:159 , ASN C:8 , SER C:56 , ARG C:58	BINDING SITE FOR RESIDUE SO4 A 406
7	AC7	SOFTWARE	ARG B:78 , ARG C:78	BINDING SITE FOR RESIDUE SO4 C 407

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:81	-	Pro A:82
2	Glu B:81	-	Pro B:82
3	Glu C:81	-	Pro C:82
4	Glu D:81	-	Pro D:82

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

(no "PROSITE Motif" information available for 1RFZ)

(no "Exon" information available for 1RFZ)

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:164
 aligned with P84133_GEOSE | P84133 from UniProtKB/TrEMBL  Length:168

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         P84133_GEOSE     1 SNAMSEFIMNNLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTMEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRA 164
               SCOP domains d1rfza_ A: YutG homologue                                                                                                                                            SCOP domains
               CATH domains 1rfzA00 A:-2-161 YutG-like                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfz A  -2 SNAmSEFImNNLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTmEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRA 161
                               |    |7        17        27        37      | 47        57        67        77        87        97       107       117       127       137       147       157    
                               |    |                                    44-MSE                                                                                                                 
                               1-MSE|                                                                                                                                                           
                                    6-MSE

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with P84133_GEOSE | P84133 from UniProtKB/TrEMBL  Length:168

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         P84133_GEOSE     1 SNAMSEFIMNNLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTMEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRA 164
               SCOP domains d1rfzb_ B: YutG homologue                                                                                                                                            SCOP domains
               CATH domains 1rfzB00 B:-2-161 YutG-like                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfz B  -2 SNAmSEFImNNLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTmEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRA 161
                               |    |7        17        27        37      | 47        57        67        77        87        97       107       117       127       137       147       157    
                               1-MSE|                                    44-MSE                                                                                                                 
                                    6-MSE

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with P84133_GEOSE | P84133 from UniProtKB/TrEMBL  Length:168

    Alignment length:161
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164 
         P84133_GEOSE     5 SEFIMNNLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTMEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRAA 165
               SCOP domains d1rfzc_ C: YutG homologue                                                                                                                                         SCOP domains
               CATH domains 1rfzC00 C:2-162 YutG-like                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfz C   2 SEFImNNLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTmEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRAA 162
                                |   11        21        31        41  |     51        61        71        81        91       101       111       121       131       141       151       161 
                                6-MSE                                44-MSE

Chain D from PDB  Type:PROTEIN  Length:154
 aligned with P84133_GEOSE | P84133 from UniProtKB/TrEMBL  Length:168

    Alignment length:154
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         P84133_GEOSE    11 NLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTMEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRA 164
               SCOP domains d1rfzd_ D: YutG homologue                                                                                                                                  SCOP domains
               CATH domains 1rfzD00 D:8-161 YutG-like                                                                                                                                  CATH domains
           Pfam domains (1) ----PgpA-1rfzD01 D:12-159                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) ----PgpA-1rfzD02 D:12-159                                                                                                                               -- Pfam domains (2)
           Pfam domains (3) ----PgpA-1rfzD03 D:12-159                                                                                                                               -- Pfam domains (3)
           Pfam domains (4) ----PgpA-1rfzD04 D:12-159                                                                                                                               -- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfz D   8 NLEQTARRWLEERGVTVEKIAELVYYLQSKYHPDLTmEECIENVNRVISKREVQNAILTGIQLDKLAEDGRLDEPLQSIIRRDEGLYGVDEILALSIVNVYGSIGFTNYGYIDKQKPGILQYLNDKSTGKCNTFLDDIVGAIAAAASSRLAHRA 161
                                    17        27        37      | 47        57        67        77        87        97       107       117       127       137       147       157    
                                                               44-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: YutG-like (3)

Superfamily: YutG-like (3)

Family: YutG-like (3)

Protein domain: YutG homologue (1)

Bacillus stearothermophilus [TaxId: 1422] (1)

1a	d1rfza_	A:
1b	d1rfzb_	B:
1c	d1rfzc_	C:
1d	d1rfzd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: YutG-like (3)

Homologous Superfamily: YutG-like (3)

Geobacillus stearothermophilus. Organism_taxid: 1422. (1)

1a	1rfzC00	C:2-162
1b	1rfzA00	A:-2-161
1c	1rfzB00	B:-2-161
1d	1rfzD00	D:8-161

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PgpA] (3)

Family: PgpA (3)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (1)

1a	PgpA-1rfzD01	D:12-159
1b	PgpA-1rfzD02	D:12-159
1c	PgpA-1rfzD03	D:12-159
1d	PgpA-1rfzD04	D:12-159

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (P84133_GEOSE | P84133)

molecular function
	GO:0008962	phosphatidylglycerophosphatase activity	Catalysis of the reaction: phosphatidylglycerophosphate + H2O = phosphatidylglycerol + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:81 - Pro A:82	[ RasMol ]
		Glu B:81 - Pro B:82	[ RasMol ]
		Glu C:81 - Pro C:82	[ RasMol ]
		Glu D:81 - Pro D:82	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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