3GJB - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CYTC3 WITH FE(II) AND ALPHA-KETOGLUTARATE

Authors :   C. Wong, C. L. Drennan

Date :   08 Mar 09 (Deposition) - 14 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)

Keywords :   Cytc3, Halogenase, Beta Barrel, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Wong, D. G. Fujimori, C. T. Walsh, C. L. Drennan
Structural Analysis Of An Open Active Site Conformation Of Nonheme Iron Halogenase Cytc3
J. Am. Chem. Soc. V. 131 4872 2009
PubMed-ID: 19281171 | Reference-DOI: 10.1021/JA8097355

Molecule 1 - CYTC3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CYTC3
	Organism Scientific	:	STREPTOMYCES SP.
	Organism Taxid	:	1931
	Strain	:	PSPHE02

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 15)

No.	Name	Count	Type	Full Name
1	ACT	8	Ligand/Ion	ACETATE ION
2	AKG	3	Ligand/Ion	2-OXOGLUTARIC ACID
3	FE2	2	Ligand/Ion	FE (II) ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
3	FE2	1	Ligand/Ion	FE (II) ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	ACT	5	Ligand/Ion	ACETATE ION
2	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
3	FE2	1	Ligand/Ion	FE (II) ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 30)

No.	Name	Count	Type	Full Name
1	ACT	16	Ligand/Ion	ACETATE ION
2	AKG	6	Ligand/Ion	2-OXOGLUTARIC ACID
3	FE2	4	Ligand/Ion	FE (II) ION
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:118 , HIS A:240 , AKG A:321 , HOH A:400 , HOH A:402	BINDING SITE FOR RESIDUE FE2 A 320
02	AC2	SOFTWARE	LYS A:108 , THR A:115 , HIS A:118 , HIS A:240 , SER A:242 , ARG A:253 , FE2 A:320 , ACT A:325 , HOH A:335 , HOH A:400 , HOH A:402	BINDING SITE FOR RESIDUE AKG A 321
03	AC3	SOFTWARE	LYS A:62 , ARG A:102 , ALA A:121 , THR A:122 , PHE A:123 , ALA A:124 , HIS A:125 , GLN A:131 , ARG A:259 , ASP A:279 , ASP B:116 , SO4 B:327	BINDING SITE FOR RESIDUE AKG A 322
04	AC4	SOFTWARE	HIS A:299	BINDING SITE FOR RESIDUE ACT A 323
05	AC5	SOFTWARE	LYS A:62 , HIS A:125 , GLY B:114 , THR B:115 , ASP B:116 , SO4 B:327	BINDING SITE FOR RESIDUE ACT A 324
06	AC6	SOFTWARE	ALA A:120 , SER A:236 , ARG A:259 , AKG A:321 , SO4 B:327	BINDING SITE FOR RESIDUE ACT A 325
07	AC7	SOFTWARE	ASP A:116 , HOH A:347 , LYS B:62 , TYR B:68 , GLU B:104 , ARG B:259 , AKG B:321 , ACT B:323 , ACT B:325	BINDING SITE FOR RESIDUE SO4 A 326
08	AC8	SOFTWARE	HIS B:118 , HIS B:240 , HOH B:410 , HOH B:411 , HOH B:412 , HOH B:413	BINDING SITE FOR RESIDUE FE2 B 320
09	AC9	SOFTWARE	ASP A:116 , SO4 A:326 , LYS B:62 , ARG B:102 , ALA B:121 , THR B:122 , PHE B:123 , ALA B:124 , HIS B:125 , GLN B:131 , ARG B:259 , ASP B:279	BINDING SITE FOR RESIDUE AKG B 321
10	BC1	SOFTWARE	LYS B:108 , GLY B:161 , SER B:242 , ARG B:253 , HOH B:413	BINDING SITE FOR RESIDUE ACT B 322
11	BC2	SOFTWARE	ASP A:116 , SO4 A:326 , LYS B:62 , HIS B:125	BINDING SITE FOR RESIDUE ACT B 323
12	BC3	SOFTWARE	GLN B:266 , HIS B:299 , HOH B:427	BINDING SITE FOR RESIDUE ACT B 324
13	BC4	SOFTWARE	SO4 A:326 , SER B:236 , ARG B:259 , HOH B:412	BINDING SITE FOR RESIDUE ACT B 325
14	BC5	SOFTWARE	HIS B:155 , THR B:157	BINDING SITE FOR RESIDUE ACT B 326
15	BC6	SOFTWARE	LYS A:62 , TYR A:68 , GLU A:104 , AKG A:322 , ACT A:324 , ACT A:325 , ASP B:116 , HOH B:430	BINDING SITE FOR RESIDUE SO4 B 327

(no "SS Bond" information available for 3GJB)

Asymmetric Unit

No.	Residues
1	Gly A:27	-	Pro A:28
2	Gly B:27	-	Pro B:28

(no "SAP(SNP)/Variant" information available for 3GJB)

(no "PROSITE Motif" information available for 3GJB)

(no "Exon" information available for 3GJB)

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:260
 aligned with D0VX22_STRSQ | D0VX22 from UniProtKB/TrEMBL  Length:319

    Alignment length:310
                                    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
         D0VX22_STRSQ     8 ANFTFSPEEVARFERDGYIGPVKIFEPEEMTRRWNIIRRQLLDRSLAIYPDSNGKANISNYDRHLDIDLLAEHIMRPEIVDRVGSLIGRNLLCWRSEFFPKYQGDEGTDWHQAATFAHATGKPQIIWPSDEGRPAFIGTITVWTAFTHSTEQNGCLQLMPGTHTSMNYDESKGMDYDADAINQREKDGIKRGFFGYDYRSLQKDPDWKPDESQAYPMVLKPGEAVIFWSNTMHASLPHTGSKTDYRMGFAARYVPTQVQVYPGTENLTEYGDGINLEKYGAVLTSGVDEYGHNRIARTSQRGYEFVPRQI 317
               SCOP domains d3gjba_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhheeeeee..hhhhhhhhhhhhhhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeeee...........ee....--..ee...eeeeee..........eee....----...--------------------------------------------.........eeeeee....eee..........eeeeeeeeee...ee........eee..ee.hhh..eeee......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gjb A   8 ANFTFSPEEVARFERDGYIGPVKIFEPEEMTRRWNIIRRQLLDRSLAIYPDSNGKANISNYDRHLDIDLLAEHIMRPEIVDRVGSLIGRNLLCWRSEFFPKYQGDEGTDWHQAATFAHATGKPQIIWPSD--RPAFIGTITVWTAFTHSTEQNGCLQLMPGT----NYD--------------------------------------------AYPMVLKPGEAVIFWSNTMHASLPHTGSKTDYRMGFAARYVPTQVQVYPGTENLTEYGDGINLEKYGAVLTSGVDEYGHNRIARTSQRGYEFVPRQI 317
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  |    147       157       167 |    | |-         -         -         -         -   |   227       237       247       257       267       277       287       297       307       317
                                                                                                                                                           137  |                          169  174 |                                          221                                                                                                
                                                                                                                                                              140                                 176

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with D0VX22_STRSQ | D0VX22 from UniProtKB/TrEMBL  Length:319

    Alignment length:312
                                    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  
         D0VX22_STRSQ     8 ANFTFSPEEVARFERDGYIGPVKIFEPEEMTRRWNIIRRQLLDRSLAIYPDSNGKANISNYDRHLDIDLLAEHIMRPEIVDRVGSLIGRNLLCWRSEFFPKYQGDEGTDWHQAATFAHATGKPQIIWPSDEGRPAFIGTITVWTAFTHSTEQNGCLQLMPGTHTSMNYDESKGMDYDADAINQREKDGIKRGFFGYDYRSLQKDPDWKPDESQAYPMVLKPGEAVIFWSNTMHASLPHTGSKTDYRMGFAARYVPTQVQVYPGTENLTEYGDGINLEKYGAVLTSGVDEYGHNRIARTSQRGYEFVPRQIPS 319
               SCOP domains d3gjbb_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhheeeeee..hhhhhhhhhhhhhhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeeee...........ee....--.......eeeeee..........eee........ee..---------------------------------------.............eeeeee....eee..........eeeeeeeeee...ee........eee..ee.hhh..ee............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gjb B   8 ANFTFSPEEVARFERDGYIGPVKIFEPEEMTRRWNIIRRQLLDRSLAIYPDSNGKANISNYDRHLDIDLLAEHIMRPEIVDRVGSLIGRNLLCWRSEFFPKYQGDEGTDWHQAATFAHATGKPQIIWPSD--RPAFIGTITVWTAFTHSTEQNGCLQLMPGTHTSMNYDE---------------------------------------DESQAYPMVLKPGEAVIFWSNTMHASLPHTGSKTDYRMGFAARYVPTQVQVYPGTENLTEYGDGINLEKYGAVLTSGVDEYGHNRIARTSQRGYEFVPRQIPS 319
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  |    147       157       167       177         -         -         -       217       227       237       247       257       267       277       287       297       307       317  
                                                                                                                                                           137  |                                  177                                     217                                                                                                      
                                                                                                                                                              140

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: PhyH-like (5)

Protein domain: automated matches (1)

Streptomyces sp. [TaxId: 1931] (1)

1a	d3gjba_	A:
1b	d3gjbb_	B:

(no "CATH Domain" information available for 3GJB)

(no "Pfam Domain" information available for 3GJB)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3GJB)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:27 - Pro A:28	[ RasMol ]
		Gly B:27 - Pro B:28	[ RasMol ]

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	D0VX22_STRSQ \| D0VX22	:	3gja

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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