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Title :   ACTIVE SEMISYNTHETIC [FEFE]-HYDROGENASE CPI WITH AZA-DITHIOLATO-BRIDGED [2FE] COFACTOR

Authors :   J. Esselborn, E. Hofmann, G. Kurisu, T. Happe

Date :   19 Dec 14 (Deposition) - 11 Nov 15 (Release) - 11 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Hydrogenase, H-Cluster, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Esselborn, N. Muraki, K. Klein, V. Engelbrecht, N. Metzler-Nolte, U. -P. Apfel, E. Hofmann, G. Kurisu, T. Happe
A Structural View Of Synthetic Cofactor Integration Into [Fefe]-Hydrogenases
Chem Sci 2015
PubMed: search | Reference-DOI: 10.1039/C5SC03397G

Molecule 1 - IRON HYDROGENASE 1
	Chains	:	A, B
	EC Number	:	1.12.7.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	CLOSTRIDIUM PASTEURIANUM
	Organism Taxid	:	1501
	Synonym	:	CPI,FE-ONLY HYDROGENASE,[FE] HYDROGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 17)

No.	Name	Count	Type	Full Name
1	402	2	Ligand/Ion	DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU-(IMINODIMETHANETHIOLATATO-1KAPPAS:2KAPPAS)-MU-(OXOMETHYLIDENE)DIIRON(2+)
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	MG	5	Ligand/Ion	MAGNESIUM ION
4	SF4	8	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	402	1	Ligand/Ion	DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU-(IMINODIMETHANETHIOLATATO-1KAPPAS:2KAPPAS)-MU-(OXOMETHYLIDENE)DIIRON(2+)
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SF4	4	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	402	2	Ligand/Ion	DICARBONYL[BIS(CYANIDE-KAPPAC)]-MU-(IMINODIMETHANETHIOLATATO-1KAPPAS:2KAPPAS)-MU-(OXOMETHYLIDENE)DIIRON(2+)
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SF4	8	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:230 , PRO A:231 , SER A:232 , ILE A:268 , ALA A:272 , CYS A:299 , PRO A:324 , GLN A:325 , MET A:353 , PRO A:354 , CYS A:355 , LYS A:358 , PHE A:417 , MET A:497 , CYS A:503 , SF4 A:602	binding site for residue 402 A 601
02	AC2	SOFTWARE	CYS A:300 , PRO A:301 , CYS A:355 , CYS A:499 , CYS A:503 , GLY A:506 , 402 A:601	binding site for residue SF4 A 602
03	AC3	SOFTWARE	CYS A:157 , THR A:163 , MET A:166 , CYS A:190 , LEU A:191 , LEU A:192 , CYS A:193 , GLY A:194 , CYS A:196	binding site for residue SF4 A 603
04	AC4	SOFTWARE	CYS A:147 , LEU A:148 , CYS A:150 , GLY A:151 , CYS A:153 , CYS A:200 , VAL A:202 , LEU A:205	binding site for residue SF4 A 604
05	AC5	SOFTWARE	HIS A:94 , GLU A:95 , LYS A:97 , CYS A:98 , CYS A:101 , CYS A:107 , LYS A:146 , VAL A:202 , ALA A:203	binding site for residue SF4 A 605
06	AC6	SOFTWARE	LEU A:33 , CYS A:34 , PHE A:35 , CYS A:46 , GLU A:47 , CYS A:49 , CYS A:62	binding site for residue FES A 606
07	AC7	SOFTWARE	LEU A:218 , HOH A:751 , HOH A:766 , HOH A:1057 , HOH A:1063 , HOH A:1119	binding site for residue MG A 607
08	AC8	SOFTWARE	ASN A:40 , ASP A:42 , HOH A:1041 , HOH A:1050 , HOH A:1101 , HOH B:1062	binding site for residue MG A 608
09	AC9	SOFTWARE	GLU A:456 , HOH A:701 , HOH A:722 , HOH A:743 , HOH A:789 , HOH A:1247	binding site for residue MG A 609
10	AD1	SOFTWARE	ALA B:230 , PRO B:231 , SER B:232 , ILE B:268 , ALA B:272 , CYS B:299 , PRO B:324 , GLN B:325 , MET B:353 , PRO B:354 , CYS B:355 , LYS B:358 , PHE B:417 , MET B:497 , CYS B:503 , SF4 B:602	binding site for residue 402 B 601
11	AD2	SOFTWARE	CYS B:300 , PRO B:301 , CYS B:355 , CYS B:499 , CYS B:503 , GLY B:506 , 402 B:601	binding site for residue SF4 B 602
12	AD3	SOFTWARE	CYS B:157 , MET B:166 , CYS B:190 , LEU B:191 , LEU B:192 , CYS B:193 , GLY B:194 , CYS B:196	binding site for residue SF4 B 603
13	AD4	SOFTWARE	CYS B:147 , LEU B:148 , CYS B:150 , GLY B:151 , CYS B:153 , CYS B:200 , VAL B:202 , LEU B:205	binding site for residue SF4 B 604
14	AD5	SOFTWARE	HIS B:94 , GLU B:95 , LYS B:97 , CYS B:98 , CYS B:101 , CYS B:107 , VAL B:202 , ALA B:203	binding site for residue SF4 B 605
15	AD6	SOFTWARE	LEU B:33 , CYS B:34 , PHE B:35 , LYS B:45 , CYS B:46 , GLU B:47 , CYS B:49 , CYS B:62	binding site for residue FES B 606
16	AD7	SOFTWARE	LEU B:218 , HOH B:827 , HOH B:835 , HOH B:1134 , HOH B:1196 , HOH B:1232	binding site for residue MG B 607
17	AD8	SOFTWARE	HOH B:1119 , HOH B:1306 , HOH B:1340	binding site for residue MG B 608

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

Asymmetric Unit

No.	Residues
1	Gly A:291	-	Pro A:292
2	Phe A:293	-	Pro A:294
3	His A:579	-	Pro A:580
4	Gly B:291	-	Pro B:292
5	Phe B:293	-	Pro B:294

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

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

(no "Exon" information available for 4XDC)

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:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee....hhhhhhhhh.......................eeee...eeee..........eee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..........hhhh.ee.....eeee.hhh...hhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhh.....hhhhhh.....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhh.eeeeeee..hhhhhhhh....ee..ee...eeeehhhhhhhhhhh..hhhhh.....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhh....eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdc A   1 MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQ 581
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580

Chain B from PDB  Type:PROTEIN  Length:578
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....hhhhhhhhh.......................eeee...eeee.hhh.....eeee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..........hhhh.ee.....eeee.......hhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhh.....hhhhhhh....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhh.eeeeeee..hhhhhhhh....ee..ee...eeeehhhhhhhhhhh..hhhhh.....hhhhh..hhhhhh....hhhhhhhhhhhhhhhh........hhhhh....eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdc B   2 KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSH 579
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571

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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		402	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gly A:291 - Pro A:292	[ RasMol ]
		Gly B:291 - Pro B:292	[ RasMol ]
		His A:579 - Pro A:580	[ RasMol ]
		Phe A:293 - Pro A:294	[ RasMol ]
		Phe B:293 - Pro B:294	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	4xdc
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	1.12.7.2
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	PHF1_CLOPA \| P29166	:	1c4a 1c4c 1feh 3c8y 4xdd 5byq 5byr 5bys 5la3

4xdc	D_1000205324 IS THE APO FORM OF THIS PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (8, 8)

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