3O1L - JenaLib

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Title :   CRYSTAL STRUCTURE OF A FORMYLTETRAHYDROFOLATE DEFORMYLASE (PSPTO_4314) FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000 AT 2.20 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   21 Jul 10 (Deposition) - 15 Sep 10 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B  (2x)
Biol. Unit 4: A,B  (2x)

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Formyltetrahydrofolate Deformylase (Pspto_4314) From Pseudomonas Syringae Pv. Tomato Str. Dc3000 At 2. 20 A Resolution
To Be Published
PubMed: search

Molecule 1 - FORMYLTETRAHYDROFOLATE DEFORMYLASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PURU-3, PSPTO4314, PSPTO_4314
	Organism Scientific	:	PSEUDOMONAS SYRINGAE PV. TOMATO
	Organism Taxid	:	323
	Strain	:	DC3000

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:		B
Biological Unit 4 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 33)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 36)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 30)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 66)

No.	Name	Count	Type	Full Name
1	GOL	16	Ligand/Ion	GLYCEROL
2	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	18	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:-3 , ASP A:12 , ARG A:13 , VAL A:14 , ILE A:16 , VAL A:17 , HOH A:465 , ILE B:31	BINDING SITE FOR RESIDUE GOL A 300
02	AC2	SOFTWARE	GLN A:-1 , ARG A:13 , GLU A:73 , HOH A:443	BINDING SITE FOR RESIDUE GOL A 302
03	AC3	SOFTWARE	ASP A:77 , ARG A:79 , LEU A:273 , VAL A:274	BINDING SITE FOR RESIDUE GOL A 304
04	AC4	SOFTWARE	HIS A:37 , ASP A:39 , HIS A:275 , LYS A:278 , HOH A:405	BINDING SITE FOR RESIDUE GOL A 305
05	AC5	SOFTWARE	ARG A:242 , HOH A:356 , HOH A:367 , HOH A:493 , HOH A:578 , SER B:35 , HIS B:36 , ARG B:242 , HOH B:361 , HOH B:454 , HOH B:495	BINDING SITE FOR RESIDUE SO4 A 308
06	AC6	SOFTWARE	MSE A:172 , HIS A:192 , ALA A:201 , LYS A:202 , PRO A:203	BINDING SITE FOR RESIDUE SO4 A 309
07	AC7	SOFTWARE	SER A:94 , ASN A:122 , HIS A:123 , MSE A:172 , GLN A:173	BINDING SITE FOR RESIDUE SO4 A 311
08	AC8	SOFTWARE	ARG A:95 , HIS A:123 , GLN A:124 , ASP A:125 , HIS A:139	BINDING SITE FOR RESIDUE SO4 A 313
09	AC9	SOFTWARE	PHE A:251 , ASP A:254 , MSE B:258 , ARG B:262	BINDING SITE FOR RESIDUE SO4 A 314
10	BC1	SOFTWARE	HIS A:-7 , ARG A:13 , SER A:42 , GLY A:43 , TRP A:44	BINDING SITE FOR RESIDUE SO4 A 316
11	BC2	SOFTWARE	ALA B:9 , ASP B:77 , TRP B:78 , ARG B:79 , LEU B:273 , HOH B:377	BINDING SITE FOR RESIDUE GOL B 301
12	BC3	SOFTWARE	TRP A:30 , ILE A:31 , ASP B:12 , ARG B:13 , VAL B:14 , ILE B:16 , VAL B:17 , PHE B:45 , HOH B:401 , HOH B:418	BINDING SITE FOR RESIDUE GOL B 303
13	BC4	SOFTWARE	ALA A:18 , LYS A:19 , ASN A:22 , ASN B:22	BINDING SITE FOR RESIDUE GOL B 306
14	BC5	SOFTWARE	TRP B:107 , HIS B:108 , ASP B:110	BINDING SITE FOR RESIDUE GOL B 307
15	BC6	SOFTWARE	SER B:94 , ARG B:95 , ASN B:122 , HIS B:123 , GLN B:173	BINDING SITE FOR RESIDUE SO4 B 310
16	BC7	SOFTWARE	MSE B:172 , HIS B:192 , ALA B:201 , LYS B:202 , HOH B:487	BINDING SITE FOR RESIDUE SO4 B 312
17	BC8	SOFTWARE	LEU B:60 , ARG B:64 , GLN B:85	BINDING SITE FOR RESIDUE SO4 B 315

(no "SS Bond" information available for 3O1L)

Asymmetric Unit

No.	Residues
1	Leu A:195	-	Pro A:196
2	Leu B:195	-	Pro B:196

(no "SAP(SNP)/Variant" information available for 3O1L)

(no "PROSITE Motif" information available for 3O1L)

(no "Exon" information available for 3O1L)

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:298
 aligned with Q87X74_PSESM | Q87X74 from UniProtKB/TrEMBL  Length:283

    Alignment length:298
                                           1                                                                                                                                                                                                                                                                                          
                                     -     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275        
         Q87X74_PSESM     - ---------------MRTFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHEIRADTLPFDLDGFREAFTPIAEEFSMDWRITDSAQKKRVVLMASRESHCLADLLHRWHSDELDCDIACVISNHQDLRSMVEWHDIPYYHVPVDPKDKEPAFAEVSRLVGHHQADVVVLARYMQILPPQLCREYAHQVINIHHSFLPSFVGAKPYHQASLRGVKLIGATCHYVTEELDAGPIIEQDVVRVSHRDSIENMVRFGRDVEKMVLARGLRAHLEDRVLVHDNKTVVFD 283
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhh...eeeeeeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh.eeeeee.....eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhh....eee.......hhhhhhhhhhhhhhh...eeee.........hhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o1l A -14 KIHHHHHHENLYFQGmRTFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFmRHEIRADTLPFDLDGFREAFTPIAEEFSmDWRITDSAQKKRVVLmASRESHCLADLLHRWHSDELDCDIACVISNHQDLRSmVEWHDIPYYHVPVDPKDKEPAFAEVSRLVGHHQADVVVLARYmQILPPQLCREYAHQVINIHHSFLPSFVGAKPYHQASLRGVKLIGATCHYVTEELDAGPIIEQDVVRVSHRDSIENmVRFGRDVEKmVLARGLRAHLEDRVLVHDNKTVVFD 283
                                    -5     |   5        15        25        35        45 |      55        65        75|       85      | 95       105       115       125   |   135       145       155       165      |175       185       195       205       215       225       235       245  |    255  |    265       275        
                                           1-MSE                                        47-MSE                       76-MSE          92-MSE                              129-MSE                                    172-MSE                                                                     248-MSE   258-MSE

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with Q87X74_PSESM | Q87X74 from UniProtKB/TrEMBL  Length:283

    Alignment length:285
                              1                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     
         Q87X74_PSESM     - --MRTFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFMRHEIRADTLPFDLDGFREAFTPIAEEFSMDWRITDSAQKKRVVLMASRESHCLADLLHRWHSDELDCDIACVISNHQDLRSMVEWHDIPYYHVPVDPKDKEPAFAEVSRLVGHHQADVVVLARYMQILPPQLCREYAHQVINIHHSFLPSFVGAKPYHQASLRGVKLIGATCHYVTEELDAGPIIEQDVVRVSHRDSIENMVRFGRDVEKMVLARGLRAHLEDRVLVHDNKTVVFD 283
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----ACT-3o1lB01 B:4-66                                             --------------------Formyl_trans_N-3o1lB03 B:87-264                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) -----ACT-3o1lB02 B:4-66                                             --------------------Formyl_trans_N-3o1lB04 B:87-264                                                                                                                                                   ------------------- Pfam domains (2)
         Sec.struct. author ....eeeeeeeee...hhhhhhhhhhhhh...eeeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhh..eeeeee.....eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhh...eee.......hhhhhhhhhhhhhhh...eeee.........hhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o1l B  -1 QGmRTFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFFmRHEIRADTLPFDLDGFREAFTPIAEEFSmDWRITDSAQKKRVVLmASRESHCLADLLHRWHSDELDCDIACVISNHQDLRSmVEWHDIPYYHVPVDPKDKEPAFAEVSRLVGHHQADVVVLARYmQILPPQLCREYAHQVINIHHSFLPSFVGAKPYHQASLRGVKLIGATCHYVTEELDAGPIIEQDVVRVSHRDSIENmVRFGRDVEKmVLARGLRAHLEDRVLVHDNKTVVFD 283
                              |      8        18        28        38        48        58        68       |78        88   |    98       108       118       128|      138       148       158       168   |   178       188       198       208       218       228       238       248       258       268       278     
                              1-MSE                                        47-MSE                       76-MSE          92-MSE                              129-MSE                                    172-MSE                                                                     248-MSE   258-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 '\|'

(no "SCOP Domain" information available for 3O1L)

(no "CATH Domain" information available for 3O1L)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ACT (34)

Family: ACT (19)

Pseudomonas syringae pv. tomato str. DC3000 (1)

1a	ACT-3o1lB01	B:4-66
1b	ACT-3o1lB02	B:4-66

Clan: no clan defined [family: Formyl_trans_N] (25)

Family: Formyl_trans_N (25)

Pseudomonas syringae pv. tomato str. DC3000 (1)

2a	Formyl_trans_N-3o1lB03	B:87-264
2b	Formyl_trans_N-3o1lB04	B:87-264

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q87X74_PSESM | Q87X74)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0008864	formyltetrahydrofolate deformylase activity	Catalysis of the reaction: 10-formyltetrahydrofolate + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + formate + H(+).
	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:0016742	hydroxymethyl-, formyl- and related transferase activity	Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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		Leu A:195 - Pro A:196	[ RasMol ]
		Leu B:195 - Pro B:196	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 33)

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