4X8E - JenaLib

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Title :   ERGOTHIONEINE-BIOSYNTHETIC SULFOXIDE SYNTHASE EGTB IN COMPLEX WITH N, N,N-TRIMETHYL-HISTIDINE

Authors :   A. Vit, K. V. Goncharenko, W. Blankenfeldt, F. P. Seebeck

Date :   10 Dec 14 (Deposition) - 28 Jan 15 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Ergothioneine Biosynthesis, C-Lectin, Dinb, Non-Heme Fe(Ii) Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. V. Goncharenko, A. Vit, W. Blankenfeldt, F. P. Seebeck
Structure Of The Sulfoxide Synthase Egtb From The Ergothioneine Biosynthetic Pathway.
Angew. Chem. Int. Ed. Engl. V. 54 2821 2015
PubMed-ID: 25597398 | Reference-DOI: 10.1002/ANIE.201410045

Molecule 1 - SULFOXIDE SYNTHASE EGTB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET19M
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 3-446
	Gene	:	KEK_08772
	Organism Scientific	:	MYCOBACTERIUM THERMORESISTIBILE ATCC 19527
	Organism Taxid	:	1078020
	Other Details	:	THE FIRST 2 AMINO ACIDS GH ARE FROM A TEV PROTEASE CLEAVAGE SITE. SOME N- AND C-TERMINAL RESIDUES ARE NOT VISIBLE IN THE ELCETRON DENSITY AND HAVE NOT BEEN BUILT.

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 27)

No.	Name	Count	Type	Full Name
1	AVJ	2	Ligand/Ion	N,N,N-TRIMETHYL-HISTIDINE
2	CA	2	Ligand/Ion	CALCIUM ION
3	CL	7	Ligand/Ion	CHLORIDE ION
4	FE	2	Ligand/Ion	FE (III) ION
5	GOL	12	Ligand/Ion	GLYCEROL
6	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	AVJ	1	Ligand/Ion	N,N,N-TRIMETHYL-HISTIDINE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	FE	-1	Ligand/Ion	FE (III) ION
5	GOL	8	Ligand/Ion	GLYCEROL
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	AVJ	1	Ligand/Ion	N,N,N-TRIMETHYL-HISTIDINE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	FE	-1	Ligand/Ion	FE (III) ION
5	GOL	4	Ligand/Ion	GLYCEROL
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:134 , GLN A:137 , HIS A:138 , TYR A:377 , TYR A:380 , ASN A:414 , TRP A:415 , GOL A:505 , FE A:515 , HOH A:702 , HOH A:712 , HOH A:771 , HOH A:782 , HOH A:826 , HOH A:883 , HOH A:1259	binding site for residue AVJ A 501
02	AC2	SOFTWARE	ARG A:22 , ARG A:25 , LEU A:26 , HOH A:802	binding site for residue GOL A 502
03	AC3	SOFTWARE	SER A:172 , ALA A:289 , GLY A:290 , TRP A:431 , HOH A:607 , HOH A:610	binding site for residue GOL A 503
04	AC4	SOFTWARE	HIS A:200 , ILE A:297 , PRO A:370 , HOH A:792 , HOH A:962 , HOH A:1008 , HOH A:1021 , HOH A:1041	binding site for residue GOL A 504
05	AC5	SOFTWARE	ARG A:87 , THR A:141 , GLN A:144 , ASP A:416 , GLN A:422 , AVJ A:501 , HOH A:743 , HOH A:1260	binding site for residue GOL A 505
06	AC6	SOFTWARE	HIS A:51 , GLN A:55 , LEU A:58 , TRP A:59 , TYR A:80 , ASP A:81 , ALA A:82 , PHE A:83 , TYR A:377 , ARG A:379 , HOH A:837 , HOH A:925 , HOH A:1005 , HOH A:1134	binding site for residue GOL A 506
07	AC7	SOFTWARE	ALA A:82 , PHE A:83 , PHE A:384 , CL A:512 , CL A:513 , HOH A:771 , HOH A:790 , HOH A:837 , HOH A:883	binding site for residue GOL A 507
08	AC8	SOFTWARE	GLN A:251 , ARG A:421 , HOH A:754 , HOH A:789 , HOH A:1249	binding site for residue GOL A 508
09	AC9	SOFTWARE	GLY A:63 , GLY A:64 , ASP A:65 , ILE A:376 , GLN A:378	binding site for residue GOL A 509
10	AD1	SOFTWARE	ARG A:87 , ARG A:90 , CL A:513 , HOH A:717 , HOH A:883	binding site for residue CL A 510
11	AD2	SOFTWARE	HIS A:417 , PRO A:418 , HOH A:994	binding site for residue CL A 511
12	AD3	SOFTWARE	PHE A:384 , TYR A:393 , GOL A:507 , HOH A:757	binding site for residue CL A 512
13	AD4	SOFTWARE	ARG A:87 , ARG A:90 , GOL A:507 , CL A:510	binding site for residue CL A 513
14	AD5	SOFTWARE	GLY A:389 , SER A:390 , GLY A:391	binding site for residue CL A 514
15	AD6	SOFTWARE	HIS A:51 , HIS A:134 , HIS A:138 , AVJ A:501 , HOH A:702 , HOH A:712	binding site for residue FE A 515
16	AD7	SOFTWARE	GLN A:353 , MET A:354 , GLY A:356 , VAL A:358 , GLU A:360 , GLY A:398 , GLY A:399 , HOH A:701	binding site for residue CA A 516
17	AD8	SOFTWARE	HOH A:666 , HOH A:668 , HOH A:687 , HOH A:698 , HOH A:943 , HOH A:966	binding site for residue MG A 517
18	AD9	SOFTWARE	HIS B:134 , GLN B:137 , HIS B:138 , TYR B:377 , TYR B:380 , ASN B:414 , TRP B:415 , FE B:508 , HOH B:644 , HOH B:691 , HOH B:733 , HOH B:788 , HOH B:886 , HOH B:985	binding site for residue AVJ B 501
19	AE1	SOFTWARE	HIS B:200 , ILE B:297 , PRO B:370 , HOH B:821 , HOH B:942	binding site for residue GOL B 502
20	AE2	SOFTWARE	ALA B:217 , ARG B:220 , TRP B:253 , PRO B:270 , HOH B:772 , HOH B:1004	binding site for residue GOL B 503
21	AE3	SOFTWARE	ARG B:22 , ARG B:25 , LEU B:26 , HOH B:716	binding site for residue GOL B 504
22	AE4	SOFTWARE	GLN B:251 , ARG B:421 , HOH B:628 , HOH B:658 , HOH B:839 , HOH B:963	binding site for residue GOL B 505
23	AE5	SOFTWARE	ARG B:87 , ARG B:90 , HOH B:919 , HOH B:985	binding site for residue CL B 506
24	AE6	SOFTWARE	HIS B:417 , PRO B:418 , HOH B:954	binding site for residue CL B 507
25	AE7	SOFTWARE	HIS B:51 , HIS B:134 , HIS B:138 , AVJ B:501 , HOH B:640 , HOH B:644	binding site for residue FE B 508
26	AE8	SOFTWARE	GLN B:353 , MET B:354 , GLY B:356 , VAL B:358 , GLU B:360 , GLY B:398 , GLY B:399 , HOH B:633	binding site for residue CA B 509
27	AE9	SOFTWARE	HOH A:1079 , HOH A:1237 , ASP B:267 , HOH B:855 , HOH B:1004 , HOH B:1025	binding site for residue MG B 510

Asymmetric Unit

No.	Residues
1	A:243	-	B:243

Asymmetric Unit

No.	Residues
1	Arg A:197	-	Pro A:198
2	Arg B:197	-	Pro B:198

(no "SAP(SNP)/Variant" information available for 4X8E)

(no "PROSITE Motif" information available for 4X8E)

(no "Exon" information available for 4X8E)

Asymmetric Unit

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Chain A from PDB  Type:PROTEIN  Length:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhhhhh...........hhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......................eeee..eeeee..........hhhhh..eeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee..eeee..........hhhhhhhhhhhhh....hhhhhhhhhhee....ee.............................hhhhh............eee...................hhhhh........eeee......hhhhh.....eee........ee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x8e A   7 PHRAELARQLIDARNRTLRLVDFDDAELRRQYDPLMSPLVWDLAHIGQQEELWLLRGGDPRRPGLLEPAVEQLYDAFVHPRASRVHLPLLSPAQARRFCATVRSAVLDALDRLPEDADTFAFGMVVSHEHQHDETMLQALNLRSGEPLLGSGTALPPGRPGVAGTSVLVPGGPFVLGVDLADEPYALDNERPAHVVDVPAFRIGRVPVTNAEWRAFIDDGGYRQRRWWSDAGWAYRCEAGLTAPQFWNPDGTRTRFGHVEDIPPDEPVQHVTYFEAEAYAAWAGARLPTEIEWEKACAWDPATGRRRRYPWGDAAPTAALANLGGDALRPAPVGAYPAGASACGAEQMLGDVWEWTSSPLRPWPGFTPMIYQRYSQPFFEGAGSGDYRVLRGGSWAVAADILRPSFRNWDHPIRRQIFAGVRLAWDVD 434
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

Chain B from PDB  Type:PROTEIN  Length:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhhhhh...........hhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh......................eeee..eeeee..........hhhhh..eeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee..eeee..........hhhhhhhhhhhh.....hhhhhhhhhhee....ee.............................hhhhh............eee...................hhhhh........eeee......hhhhh.....eee........ee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4x8e B   8 HRAELARQLIDARNRTLRLVDFDDAELRRQYDPLMSPLVWDLAHIGQQEELWLLRGGDPRRPGLLEPAVEQLYDAFVHPRASRVHLPLLSPAQARRFCATVRSAVLDALDRLPEDADTFAFGMVVSHEHQHDETMLQALNLRSGEPLLGSGTALPPGRPGVAGTSVLVPGGPFVLGVDLADEPYALDNERPAHVVDVPAFRIGRVPVTNAEWRAFIDDGGYRQRRWWSDAGWAYRCEAGLTAPQFWNPDGTRTRFGHVEDIPPDEPVQHVTYFEAEAYAAWAGARLPTEIEWEKACAWDPATGRRRRYPWGDAAPTAALANLGGDALRPAPVGAYPAGASACGAEQMLGDVWEWTSSPLRPWPGFTPMIYQRYSQPFFEGAGSGDYRVLRGGSWAVAADILRPSFRNWDHPIRRQIFAGVRLAWDV 433
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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	Cis Peptide Bonds
		Arg A:197 - Pro A:198	[ RasMol ]
		Arg B:197 - Pro B:198	[ RasMol ]

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	EGTB_MYCT3 \| G7CFI3	:	4x8b 4x8d

4x8b	THIS ENTRY CONTAINS EGTB IN ITS APO FORM.
4x8d	THIS ENTRY CONTAINS EGTB IN COMPLEX WITH N,N-DIMETHYL-HISTIDINE (AVI) AND GAMMA-GLUTAMYL-CYSTEINE (3GC).

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 27)

Sites (27, 27)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 3)

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