4TZZ - JenaLib

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Title :   CO-CRYSTALS OF THE TERNARY COMPLEX CONTAINING A T-BOX STEM I RNA, ITS COGNATE TRNAGLY, AND B. SUBTILIS YBXF PROTEIN, TREATED BY REMOVING LITHIUM SULFATE AND INCREASING PEG3350 CONCENTRATION FROM 20% TO 45% POST CRYSTALLIZATION

Authors :   J. Zhang, A. R. Ferre-D'Amare

Date :   11 Jul 14 (Deposition) - 10 Sep 14 (Release) - 24 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.64

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)
Biol. Unit 3: G,H,I  (1x)
Biol. Unit 4: J,K,L  (1x)

Keywords :   Rna, Riboswitch, Trna, T-Box (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Zhang, A. R. Ferre-D'Amare
Dramatic Improvement Of Crystals Of Large Rnas By Cation Replacement And Dehydration.
Structure V. 22 1363 2014
PubMed-ID: 25185828 | Reference-DOI: 10.1016/J.STR.2014.07.011

Molecule 1 - RIBOSOME-ASSOCIATED PROTEIN L7AE-LIKE
	Chains	:	A, D, G, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	RPLGB, YBAB, YBXF, BSU01090
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

Molecule 2 - ENGINEERED TRNAGLY
	Chains	:	B, E, H, K
	Engineered	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synthetic	:	YES

Molecule 3 - T-BOX STEM I RNA
	Chains	:	C, F, I, L
	Engineered	:	YES
	Organism Scientific	:	OCEANOBACILLUS IHEYENSIS
	Organism Taxid	:	182710
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F
Biological Unit 3 (1x)	:							G	H	I
Biological Unit 4 (1x)	:										J	K	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 37)

No.	Name	Count	Type	Full Name
1	MG	29	Ligand/Ion	MAGNESIUM ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G C:15	binding site for residue MG C 201
02	AC2	SOFTWARE	C C:102 , A F:39	binding site for residue MG C 202
03	AC3	SOFTWARE	A C:11 , G C:12	binding site for residue MG C 203
04	AC4	SOFTWARE	A E:9 , U E:11 , U E:12	binding site for residue MG E 101
05	AC5	SOFTWARE	G E:72 , A E:74	binding site for residue MG E 102
06	AC6	SOFTWARE	G E:43 , G E:44	binding site for residue MG E 103
07	AC7	SOFTWARE	U E:46 , C E:47 , C E:49 , G E:50	binding site for residue MG E 104
08	AC8	SOFTWARE	G E:72	binding site for residue MG E 105
09	AC9	SOFTWARE	U E:8 , A E:14	binding site for residue MG E 106
10	AD1	SOFTWARE	A C:39 , A C:46 , C F:102	binding site for residue MG F 201
11	AD2	SOFTWARE	G F:59	binding site for residue MG F 202
12	AD3	SOFTWARE	A F:36 , U F:37 , A F:71	binding site for residue MG F 203
13	AD4	SOFTWARE	G H:41	binding site for residue MG H 101
14	AD5	SOFTWARE	A H:37	binding site for residue MG H 102
15	AD6	SOFTWARE	G H:52	binding site for residue MG H 103
16	AD7	SOFTWARE	C H:27	binding site for residue MG H 104
17	AD8	SOFTWARE	U H:8 , A H:9	binding site for residue MG H 105
18	AD9	SOFTWARE	C I:102 , A L:39 , A L:46	binding site for residue MG I 201
19	AE1	SOFTWARE	A I:83 , G I:84	binding site for residue MG I 202
20	AE2	SOFTWARE	A I:11 , G I:12	binding site for residue MG I 203
21	AE3	SOFTWARE	G I:67	binding site for residue MG I 205
22	AE4	SOFTWARE	A I:39 , A I:46 , C L:102	binding site for residue MG L 201
23	AE5	SOFTWARE	A L:11 , G L:12	binding site for residue MG L 202

(no "SS Bond" information available for 4TZZ)

(no "Cis Peptide Bond" information available for 4TZZ)

(no "SAP(SNP)/Variant" information available for 4TZZ)

(no "PROSITE Motif" information available for 4TZZ)

(no "Exon" information available for 4TZZ)

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
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Chain A from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.....eehhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4tzz A   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE

Chain B from PDB  Type:RNA  Length:75
                                                                                                           
                 4tzz B   5 GAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUCGGGCGAAAGCCC  79
                                    14        24        34        44        54        64        74

Chain C from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4tzz C   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eehhhhhhhhhh.......ee....hhhhhhhhhhhhhhhh.......hhhhhhhhh.......eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4tzz D   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE

Chain E from PDB  Type:RNA  Length:75
                                                                                                           
                 4tzz E   5 GAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUCGGGCGAAAGCCC  79
                                    14        24        34        44        54        64        74

Chain F from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4tzz F   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100

Chain G from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeehhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhh.......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4tzz G   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE

Chain H from PDB  Type:RNA  Length:75
                                                                                                           
                 4tzz H   5 GAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUCGGGCGAAAGCCC  79
                                    14        24        34        44        54        64        74

Chain I from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4tzz I   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100

Chain J from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....eeehhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhh......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4tzz J   2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSmVESmKKLGKACGIEVGAAAVAIIL  82
                                    11        21        31        41        51      | 61|       71        81 
                                                                                   58-MSE                    
                                                                                       62-MSE

Chain K from PDB  Type:RNA  Length:75
                                                                                                           
                 4tzz K   5 GAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUCGGGCGAAAGCCC  79
                                    14        24        34        44        54        64        74

Chain L from PDB  Type:RNA  Length:102
                                                                                                                                      
                 4tzz L   1 GGGUGCGAUGAGAAGAAGAGUAUUAAGGAUUUACUAUGAUUAGCGACUCUAGGAUAGUGAAAGCUAGAGGAUAGUAACCUUAAGAAGGCACUUCGAGCACCC 102
                                    10        20        30        40        50        60        70        80        90       100

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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 '\|'

(no "SCOP Domain" information available for 4TZZ)

(no "CATH Domain" information available for 4TZZ)

(no "Pfam Domain" information available for 4TZZ)

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	RXL7_BACSU \| P46350	:	3v7e 4lck 4tzp 4tzv 4tzw

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 37)

Sites (23, 23)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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