2IML - JenaLib

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Title :   CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN FROM ARCHAEOGLOBUS FULGIDUS BINDING RIBOFLAVIN 5'-PHOSPHATE

Authors :   J. B. Bonanno, M. Dickey, K. T. Bain, J. Adams, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)

Date :   04 Oct 06 (Deposition) - 17 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Fmn Binding, Psi-2, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Bonanno, M. Dickey, K. T. Bain, J. Adams, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Hypothetical Protein From Archaeoglobus Fulgidus Binding Riboflavin 5'-Phosphate
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	MODIFIED PET26
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AF_1834
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GOL	8	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GOL	5	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU D:14 , ASN D:27 , ALA D:29 , PRO D:30 , ILE D:31 , GLY D:32 , LYS D:46 , LEU D:47 , TYR D:48 , ASN D:50 , ARG D:51 , THR D:52 , SER D:77 , LEU D:140 , HOH D:217 , HOH D:228 , HOH D:229 , HOH D:245 , HOH D:394	BINDING SITE FOR RESIDUE FMN D 200
02	AC2	SOFTWARE	GLU A:14 , ASN A:27 , ALA A:29 , PRO A:30 , ILE A:31 , GLY A:32 , LYS A:46 , LEU A:47 , TYR A:48 , ASN A:50 , ARG A:51 , THR A:52 , SER A:77 , LEU A:140 , HOH A:213 , HOH A:215 , HOH A:239 , HOH A:242 , HOH A:292 , HOH A:334	BINDING SITE FOR RESIDUE FMN A 200
03	AC3	SOFTWARE	ASN A:130 , SER A:134 , HOH A:274 , HOH A:306 , HOH A:308 , ASN C:130 , SER C:134	BINDING SITE FOR RESIDUE GOL A 201
04	AC4	SOFTWARE	ASN B:130 , SER B:134 , HOH B:238 , HOH B:269 , HOH B:305 , ILE D:129 , ASN D:130 , SER D:134	BINDING SITE FOR RESIDUE GOL B 201
05	AC5	SOFTWARE	ARG A:161 , TYR A:164 , TYR A:165 , HOH A:380 , ARG C:161 , TYR C:164 , TYR C:165	BINDING SITE FOR RESIDUE GOL A 202
06	AC6	SOFTWARE	ARG B:161 , TYR B:164 , TYR B:165 , GOL B:203 , GOL B:204 , ARG D:161 , TYR D:164 , TYR D:165	BINDING SITE FOR RESIDUE GOL B 202
07	AC7	SOFTWARE	ARG A:49 , ARG A:53 , SER A:109	BINDING SITE FOR RESIDUE GOL A 203
08	AC8	SOFTWARE	ARG D:49 , ARG D:53 , SER D:109	BINDING SITE FOR RESIDUE GOL D 202
09	AC9	SOFTWARE	ARG B:161 , GOL B:202 , HOH B:281 , ARG D:161	BINDING SITE FOR RESIDUE GOL B 203
10	BC1	SOFTWARE	ARG B:161 , GOL B:202 , HOH B:371 , ARG D:161	BINDING SITE FOR RESIDUE GOL B 204

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

Asymmetric Unit

No.	Residues
1	Asn A:90	-	Pro A:91
2	Asn B:90	-	Pro B:91
3	Asn C:90	-	Pro C:91
4	Asn D:90	-	Pro D:91

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

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

(no "Exon" information available for 2IML)

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
	(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:191
 aligned with O28442_ARCFU | O28442 from UniProtKB/TrEMBL  Length:189

    Alignment length:191
                                                                                                                                                                                                                      189  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |- 
         O28442_ARCFU     1 MRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAMAWCRFEAEMRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIIMEKIG--   -
               SCOP domains d2imla1 A:1-189 Hypothetical protein AF1834                                                                                                                                                  -- SCOP domains
               CATH domains 2imlA01 A:1-67,A:81-126                                            2imlA02      2imlA01 A:1-67,A:81-126                       2imlA02 A:68-80,A:127-189                                      -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeee...hhhhhhhhhhheeeeee..hhhhhhhhhhh..hhh.eee....ee....eeeeeeeeee..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iml A   1 LRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAmAWCRFEAEmRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIImEKIGEG 191
                                    10        20        30        40        50        60        70        80        90       100      |110       120       130       140       150       160       170       180    |  190 
                                                                                                                            98-MSE  107-MSE                                                                       185-MSE

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with O28442_ARCFU | O28442 from UniProtKB/TrEMBL  Length:189

    Alignment length:190
                                                                                                                                                                                                                      189 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-
         O28442_ARCFU     1 MRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAMAWCRFEAEMRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIIMEKIG-   -
               SCOP domains d2imlb_ B: Hypothetical protein AF1834                                                                                                                                                         SCOP domains
               CATH domains 2imlB01 B:1-67,B:81-126                                            2imlB02      2imlB01 B:1-67,B:81-126                       2imlB02 B:68-80,B:127-189                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeee...hhhhhhhhhhheeeeee..hhhhhhhhh....hhh.eee....ee....eeeeeeeeee..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iml B   1 LRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAmAWCRFEAEmRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIImEKIGE 190
                                    10        20        30        40        50        60        70        80        90       100      |110       120       130       140       150       160       170       180    |  190
                                                                                                                            98-MSE  107-MSE                                                                       185-MSE

Chain C from PDB  Type:PROTEIN  Length:190
 aligned with O28442_ARCFU | O28442 from UniProtKB/TrEMBL  Length:189

    Alignment length:190
                                                                                                                                                                                                                      189 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-
         O28442_ARCFU     1 MRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAMAWCRFEAEMRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIIMEKIG-   -
               SCOP domains d2imlc_ C: Hypothetical protein AF1834                                                                                                                                                         SCOP domains
               CATH domains 2imlC01 C:1-67,C:81-126                                            2imlC02      2imlC01 C:1-67,C:81-126                       2imlC02 C:68-80,C:127-189                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeee...hhhhhhhhhhheeeeee..hhhhhhhhhhh..hhh.eee....ee....eeeeeeeeee..eeeeeeeeeee........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iml C   1 LRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAmAWCRFEAEmRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIImEKIGE 190
                                    10        20        30        40        50        60        70        80        90       100      |110       120       130       140       150       160       170       180    |  190
                                                                                                                            98-MSE  107-MSE                                                                       185-MSE

Chain D from PDB  Type:PROTEIN  Length:197
 aligned with O28442_ARCFU | O28442 from UniProtKB/TrEMBL  Length:189

    Alignment length:197
                                                                                                                                                                                                                      189        
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-       
         O28442_ARCFU     1 MRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAMAWCRFEAEMRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIIMEKIG--------   -
               SCOP domains d2imld_ D: Hypothetical protein AF1834                                                                                                                                                                SCOP domains
               CATH domains 2imlD01 D:1-67,D:81-125                                            2imlD02      2imlD01 D:1-67,D:81-125                      2imlD02 D:68-80,D:126-189                                       -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeeeee.....eeeeeeeeee......eeeee...hhhhhhhhhhheeeeee..hhhhhhhhhhh..hhh.eee....ee....eeeeeeeeee..eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iml D   1 LRLADFGFTDGINEIIAITENEDGSWNAAPIGIIVEDSSSDTAKAKLYRNRTRANLERSGVLFANVTDDALVFAVSSFGNLNDDWYASPNPPIIKGAmAWCRFEAEmRSGVAHLKLTDGEIIEKRVRAINRGLSAVIEALVHATRYVAIKSDERRKELLERIHYYREIVQKCGSEREKRAFEIImEKIGEGHHHHHH 197
                                    10        20        30        40        50        60        70        80        90       100      |110       120       130       140       150       160       170       180    |  190       
                                                                                                                            98-MSE  107-MSE                                                                       185-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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Split barrel-like (99)

Superfamily: FMN-binding split barrel (90)

Family: MTH863-like (3)

Protein domain: Hypothetical protein AF1834 (1)

Archaeoglobus fulgidus [TaxId: 2234] (1)

1a	d2imla1	A:1-189
1b	d2imlb_	B:
1c	d2imlc_	C:
1d	d2imld_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Methane Monooxygenase Hydroxylase; Chain G, domain 1 (192)

Homologous Superfamily: Hypothetical membrane protein ta0354_69_121. (5)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1a	2imlA02	A:68-80,A:127-189
1b	2imlB02	B:68-80,B:127-189
1c	2imlC02	C:68-80,C:127-189
1d	2imlD02	D:68-80,D:126-189

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pnp Oxidase; Chain A (68)

Homologous Superfamily: Electron Transport, Fmn-binding Protein; Chain A (67)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

2a	2imlA01	A:1-67,A:81-126
2b	2imlB01	B:1-67,B:81-126
2c	2imlC01	C:1-67,C:81-126
2d	2imlD01	D:1-67,D:81-125

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O28442_ARCFU | O28442)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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