3FWX - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF THE PEPTIDE DEFORMYLASE FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961

Authors :   R. Zhang, M. Zhou, J. Stam, W. Anderson, A. Joachimiak, Center For Str Genomics Of Infectious Diseases (Csgid)

Date :   19 Jan 09 (Deposition) - 17 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Peptide Deformylase, Structural Genomics, Csgid, Hydrolase, Niaid Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, M. Zhou, J. Stam, W. Anderson, A. Joachimiak
The Crystal Structure Of The Peptide Deformylase From Vibri Cholerae O1 Biovar El Tor
To Be Published
PubMed: search

Molecule 1 - PEPTIDE DEFORMYLASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19C
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	VIBRIO CHOLERAE O395
	Organism Taxid	:	345073
	Strain	:	STR. N16961

		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 (2, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:51 , CYS B:91 , HIS B:133 , HIS B:137	BINDING SITE FOR RESIDUE ZN B 170
2	AC2	SOFTWARE	GLN A:51 , CYS A:91 , HIS A:133 , HIS A:137	BINDING SITE FOR RESIDUE ZN A 170

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

Asymmetric Unit

No.	Residues
1	Phe A:9	-	Pro A:10
2	Phe B:9	-	Pro B:10

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

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

(no "Exon" information available for 3FWX)

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:165
 aligned with DEF1_VIBCH | Q9KVU3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:165
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
           DEF1_VIBCH     3 VLQVLTFPDDRLRTVAKPVEQVTPEIQQIVDDMLETMYAEEGIGLAATQVDIHQRIVVIDISETRDQPMVLINPEIIEKRGEDGIEEGCLSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHLAGKLFVDYLSPLKRNRIKEKLEKIKRFNE 167
               SCOP domains d3fwxa_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains 3fwxA00 A:3-167 Peptide Deformylase                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee..eeeee.........eeeee..eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwx A   3 VLQVLTFPDDRLRTVAKPVEQVTPEIQQIVDDmLETmYAEEGIGLAATQVDIHQRIVVIDISETRDQPmVLINPEIIEKRGEDGIEEGCLSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHLAGKLFVDYLSPLKRNRIKEKLEKIKRFNE 167
                                    12        22        32  |   | 42        52        62        72        82        92       102       112       122       132       142       152       162     
                                                           35-MSE                              71-MSE                                                                                            
                                                               39-MSE

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with DEF1_VIBCH | Q9KVU3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:165
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
           DEF1_VIBCH     3 VLQVLTFPDDRLRTVAKPVEQVTPEIQQIVDDMLETMYAEEGIGLAATQVDIHQRIVVIDISETRDQPMVLINPEIIEKRGEDGIEEGCLSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHLAGKLFVDYLSPLKRNRIKEKLEKIKRFNE 167
               SCOP domains d3fwxb_ B: automated matches                                                                                                                                          SCOP domains
               CATH domains 3fwxB00 B:3-167 Peptide Deformylase                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee..eeeee.........eeeee..eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwx B   3 VLQVLTFPDDRLRTVAKPVEQVTPEIQQIVDDmLETmYAEEGIGLAATQVDIHQRIVVIDISETRDQPmVLINPEIIEKRGEDGIEEGCLSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHLAGKLFVDYLSPLKRNRIKEKLEKIKRFNE 167
                                    12        22        32  |   | 42        52        62        72        82        92       102       112       122       132       142       152       162     
                                                           35-MSE                              71-MSE                                                                                            
                                                               39-MSE

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Peptide deformylase (87)

Superfamily: Peptide deformylase (87)

Family: Peptide deformylase (62)

Protein domain: automated matches (12)

Vibrio cholerae [TaxId: 345073] (1)

1a	d3fwxa_	A:
1b	d3fwxb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Peptide Deformylase (68)

Homologous Superfamily: Peptide Deformylase (68)

Vibrio cholerae o395. Organism_taxid: 345073. Strain: str. N16961. (1)

1a	3fwxA00	A:3-167
1b	3fwxB00	B:3-167

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DEF1_VIBCH | Q9KVU3)

molecular function
	GO:0008463	formylmethionine deformylase activity	Catalysis of the reaction: N-formyl-L-methionine + H(2)O = L-methionine + formate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042586	peptide deformylase activity	Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
biological process
	GO:0031365	N-terminal protein amino acid modification	The alteration of the N-terminal amino acid residue in a protein.
	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).
	GO:0043686	co-translational protein modification	The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

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