3A43 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HYPA

Authors :   S. Watanabe, T. Arai, R. Matsumi, H. Aromi, T. Imanaka, K. Miki

Date :   30 Jun 09 (Deposition) - 06 Oct 09 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   [Nife] Hydrogenase Maturation, Zinc-Finger, Nickel Binding, Metal- Binding, Nickel, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Watanabe, T. Arai, R. Matsumi, H. Atomi, T. Imanaka, K. Miki
Crystal Structure Of Hypa, A Nickel-Binding Metallochaperon For [Nife] Hydrogenase Maturation.
J. Mol. Biol. V. 394 448 2009
PubMed-ID: 19769985 | Reference-DOI: 10.1016/J.JMB.2009.09.030

Molecule 1 - HYDROGENASE NICKEL INCORPORATION PROTEIN HYPA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21(+)A
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HYPA
	Organism Common	:	THERMOCOCCUS KODAKARAENSIS
	Organism Scientific	:	PYROCOCCUS KODAKARAENSIS
	Organism Taxid	:	69014
	Strain	:	KOD1
	Synonym	:	HYPD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FME	2	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	FME	6	Mod. Amino Acid	N-FORMYLMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:73 , CYS A:76 , CYS A:110 , CYS A:113	BINDING SITE FOR RESIDUE ZN A 701
2	AC2	SOFTWARE	CYS B:73 , CYS B:76 , CYS B:110 , CYS B:113	BINDING SITE FOR RESIDUE ZN B 702

(no "SS Bond" information available for 3A43)

(no "Cis Peptide Bond" information available for 3A43)

(no "SAP(SNP)/Variant" information available for 3A43)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	2	A:34-76 B:34-76

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	1	A:34-76 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	1	- B:34-76

Biological Unit 3 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HYPA	PS01249	Hydrogenases expression/synthesis hypA family signature.	HYPA_THEKO	34-76	6	A:34-76 B:34-76

(no "Exon" information available for 3A43)

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:139
 aligned with HYPA_THEKO | Q5JIH3 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           HYPA_THEKO     1 MHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEGGS 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee..eeee.....eee.hhh.......hhhhh..hhhhhhhhh.........eeeee...eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------HYPA  PDB: A:34-76 UniProt: 34-76          --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a43 A   1 mHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEGGS 139
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130         
                            |                                                                                                                                          
                            1-FME

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with HYPA_THEKO | Q5JIH3 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           HYPA_THEKO     1 MHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIKIEKEGGS 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhh.......eeeeeee...eee.....ee......---------------------..........eee.....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------HYPA  PDB: B:34-76 UniProt: 34-76          --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a43 B   1 mHEWALADAIVRTVLDYAQREGASRVKAVRVVLGELQDVAEDIVKFAMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVK---------------------LACPKCGSHDFEVVKGRGVYVAGIKIEKEGGS 139
                            |       10        20        30        40        50        60        70        80     |   -         -       110       120       130         
                            1-FME                                                                               86                   108

Legend:		→ Mismatch	(orange background)
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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 3A43)

(no "CATH Domain" information available for 3A43)

(no "Pfam Domain" information available for 3A43)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HYPA_THEKO | Q5JIH3)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

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	3a43
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	HYPA_THEKO \| Q5JIH3
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	HYPA_THEKO \| Q5JIH3	:	3a44 5aun 5auo 5aup

Description

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