3FKH - JenaLib

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Title :   CRYSTAL STRUCTURE OF PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (NP_601736.1) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO AT 2.51 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   16 Dec 08 (Deposition) - 13 Jan 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.51

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Np_601736. 1, Putative Pyridoxamine 5'-Phosphate Oxidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Pyridoxamine 5'-Phosphate Oxidase (Np_601736. 1) From Corynebacterium Glutamicum Atcc 13032 Kitasato At 2. 51 A Resolution
To Be Published
PubMed: search

Molecule 1 - PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
	Atcc	:	13032
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CG2794, NP_601736.1
	Organism Common	:	BREVIBACTERIUM FLAVUM
	Organism Scientific	:	CORYNEBACTERIUM GLUTAMICUM ATCC 13032
	Organism Taxid	:	196627

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 24)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
4	P33	5	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
4	P33	1	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
4	P33	2	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

Biological Unit 3 (3, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
4	P33	2	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL B:27 , PHE B:36 , LEU B:57 , HIS B:64 , ALA B:87	BINDING SITE FOR RESIDUE P33 B 138
2	AC2	SOFTWARE	ASN C:6 , ILE C:7	BINDING SITE FOR RESIDUE CA C 138
3	AC3	SOFTWARE	PHE C:36 , VAL C:116	BINDING SITE FOR RESIDUE P33 C 139
4	AC4	SOFTWARE	PRO C:37 , ASN C:39 , ARG C:50 , PRO C:106 , TRP C:107 , HOH C:147 , HOH C:150	BINDING SITE FOR RESIDUE GOL C 140
5	AC5	SOFTWARE	PHE D:36	BINDING SITE FOR RESIDUE P33 D 138
6	AC6	SOFTWARE	ASN D:6 , ILE D:7 , GLU D:12	BINDING SITE FOR RESIDUE GOL D 139
7	AC7	SOFTWARE	ARG D:50 , ASP D:100 , TYR D:113 , PHE E:36 , PHE E:58 , SER E:59 , MSE E:60 , ASN E:61 , LEU E:62 , HIS E:64 , ILE E:89	BINDING SITE FOR RESIDUE P33 E 138
8	AC8	SOFTWARE	GLU C:88 , GLU E:10 , ASN E:121	BINDING SITE FOR RESIDUE GOL E 139

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

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

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

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

(no "Exon" information available for 3FKH)

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:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkhA00 A:0-132 Electron Transport, Fmn-binding Protein; Chain A                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhh...eeeeeeee..eeeeeeeeeeee..eeeeeee....eeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhhhh..........eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkh A   0 GmDNPVNILNEQEALERLQSVSLGRVVVRRSDEmDIFPVNFIVDKGAIYIRTAELNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGE 132
                             |       9        19        29   |    39        49   ||   67        77        87        97       107       117       127     
                             |                              33-MSE              53|                                                                      
                             1-MSE                                               62

Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3fkhB00 B:2-133 Electron Transport, Fmn-binding Protein; Chain A                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhh..eeeeeeee..eeeeeeeeeeee..eeeeee.hhhhhh......eeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhhhh...........eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkh B   1 mDNPVNILNEQEALERLQSVSLGRVVVRRSDEmDIFPVNFIVDKGAIYIRTAEGNKLFSmNLNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE 133
                            |       10        20        30  |     40        50        60        70        80        90       100       110       120       130   
                            1-MSE                          33-MSE                     60-MSE

Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkhC00 C:4-130 Electron Transport, Fmn-binding Protein; Chain A                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhh..eeeeeeee..eeeeeeeeeeee..eeeeee.hhhhhhhh....eeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhhh............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkh C   4 PVNILNEQEALERLQSVSLGRVVVRRSDEmDIFPVNFIVDKGAIYIRTAEGNKLFSmNLNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTL 130
                                    13        23        33        43        53      | 63        73        83        93       103       113       123       
                                                        33-MSE                     60-MSE

Chain D from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkhD00 D:0-133 Electron Transport, Fmn-binding Protein; Chain A                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhhh..eeeeeeee..eeeeeeee.eee..eeeeee.hhhhhhh.....eeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhh.............eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkh D   0 GmDNPVNILNEQEALERLQSVSLGRVVVRRSDEmDIFPVNFIVDKGAIYIRTAEGNKLFSmNLNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTLGEE 133
                             |       9        19        29   |    39        49        59|       69        79        89        99       109       119       129    
                             1-MSE                          33-MSE                     60-MSE

Chain E from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3fkhE00 E:5-130 Electron Transport, Fmn-binding Protein; Chain A                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhh.eeeeeeee..eeeeeeeeeeee..eeeeeee..hhhhhh....eeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhh............eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fkh E   5 VNILNEQEALERLQSVSLGRVVVRRSDEmDIFPVNFIVDKGAIYIRTAEGNKLFSmNLNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKPWIPTLKYNYVRIVPNEITGREFTL 130
                                    14        24        34        44        54     |  64        74        84        94       104       114       124      
                                                       33-MSE                     60-MSE

Chain F from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkhF00 F:0-132 Electron Transport, Fmn-binding Protein; Chain A                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhh...eeeeeeee..eeeeeeeeeeee..eeeeee.hhhhhhh.....eeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhhh.......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkh F   0 GmDNPVNILNEQEALERLQSVSLGRVVVRRSDEmDIFPVNFIVDKGAIYIRTAEGNKLFSmNLNHDVLFEADEVKDGKAWSVVVRATAEIVRKLDEIAYADTLELKLKYNYVRIVPNEITGREFTLGE 132
                             |       9        19        29   |    39        49        59|       69        79        89        99     ||114       124        
                             1-MSE                          33-MSE                     60-MSE                                      105|                     
                                                                                                                                    111

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

(no "SCOP Domain" information available for 3FKH)

Asymmetric Unit

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Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pnp Oxidase; Chain A (68)

Homologous Superfamily: Electron Transport, Fmn-binding Protein; Chain A (67)

Brevibacterium flavum (Corynebacterium glutamicum atcc 13032) (1)

1a	3fkhD00	D:0-133
1b	3fkhB00	B:2-133
1c	3fkhC00	C:4-130
1d	3fkhF00	F:0-132
1e	3fkhE00	E:5-130
1f	3fkhA00	A:0-132

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

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 24)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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