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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF A HYDROXYPROLINE EPIMERASE FROM AGROBACTERIUM VITIS, TARGET EFI-506420, WITH BOUND TRANS-4-OH-L-PROLINE

Authors :   M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wa S. Sojitra, M. Stead, E. Washington, A. S. Glenn, S. Chowdhury, B. Evan J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerl S. C. Almo, Enzyme Function Initiative (Efi)

Date :   20 Jun 13 (Deposition) - 17 Jul 13 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Proline Racemase Family, Proposed 3-Oh And 4-Oh Proline Epimerase, Enzyme Function Initiative, Efi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, M. Stead, E. Washington, A. S. Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of A Hydroxyproline Epimerase From Agrobacterium Vitis, Target Efi-506420, With Bound Trans-4-Oh-L-Proline
To Be Published
PubMed: search

Molecule 1 - UNCHARACTERIZED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AVI_0518
	Organism Scientific	:	AGROBACTERIUM VITIS
	Organism Taxid	:	311402
	Strain	:	S4

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	HYP	1	Mod. Residue	4-HYDROXYPROLINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:93 , GLY A:94 , SER A:95 , ASP A:251 , CYS A:255 , GLY A:256 , THR A:257 , HOH A:588	BINDING SITE FOR RESIDUE ACT A 401
2	AC2	SOFTWARE	GLY B:237 , VAL B:272	BINDING SITE FOR RESIDUE ACT B 401
3	AC3	SOFTWARE	GLN B:85 , SER B:93 , GLY B:94 , SER B:95 , ASN B:96 , TYR B:227 , ASP B:251 , CYS B:255 , GLY B:256 , THR B:257 , HOH B:537	BINDING SITE FOR RESIDUE HYP B 402

(no "SS Bond" information available for 4LB0)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:57	-	Pro A:58
2	Glu A:114	-	Pro A:115
3	Trp A:246	-	Pro A:247
4	Glu B:57	-	Pro B:58
5	Glu B:114	-	Pro B:115
6	Trp B:246	-	Pro B:247

(no "SAP(SNP)/Variant" information available for 4LB0)

(no "PROSITE Motif" information available for 4LB0)

(no "Exon" information available for 4LB0)

Asymmetric/Biological 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4lb0a_ A: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................................hhhhhhhhhhhhhhhhhhhhhhhh....................................hhhhhhhhhhhhhhh...........................................................................hhhh...hhhhhhhhhhhhhhhhhhhhhhh..........................................hhhhhhhhhhhhhhh..............................................................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lb0 A   1 MRWKRMMQLLDVHCEGEIGKVAIGGVPKIPGDTVADQLHWLNTDPKGRELRHFLVLEPRGAPIGSVNLLLPAKDSRADAAFIILQPDQAHASSGSNSICVTTALLESGMIEMQEPETVVMLETAAGLVKAVAQCRDGHCDSVTLTMVPSFVHELDAQIATESWGEIRFDLAYGGVFYALVDVRQLGLTIEPGNARRLVEAGMLLKGEINQRIQVVHPDIPAISGVAYVMFRDEDPDGAVRTCTTMWPGRVDRSPCGTGNSANLATLHARGRVKPGDSFLSRSIIGSQFTVGLQGLTTVAGRSAVIPTITGRGFTYGIHQVALDDPLGGGFVLTDVWGAAAET 344
                                    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  ||   332       342  
                                                                                                                                                                                                                                                                                                                                                            323|                  
                                                                                                                                                                                                                                                                                                                                                             326

Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4lb0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................hhhhhhhhhhhhhhhhhhhhhhhh....................................hhhhhhhhhhhhhhh...........................................................................hhhh...hhhhhhhhhhhhhhhhhhhhhhh..........................................hhhhhhhhhhhhhhh................................................................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lb0 B   0 SMRWKRMMQLLDVHCEGEIGKVAIGGVPKIPGDTVADQLHWLNTDPKGRELRHFLVLEPRGAPIGSVNLLLPAKDSRADAAFIILQPDQAHASSGSNSICVTTALLESGMIEMQEPETVVMLETAAGLVKAVAQCRDGHCDSVTLTMVPSFVHELDAQIATESWGEIRFDLAYGGVFYALVDVRQLGLTIEPGNARRLVEAGMLLKGEINQRIQVVHPDIPAISGVAYVMFRDEDPDGAVRTCTTMWPGRVDRSPCGTGNSANLATLHARGRVKPGDSFLSRSIIGSQFTVGLQGLTTVAGRSAVIPTITGRGFTYGIHQVALDAFDPLGGGFVLTDVWGAAAETIK 346
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Diaminopimelate epimerase-like (37)

Superfamily: Diaminopimelate epimerase-like (37)

Family: automated matches (15)

Protein domain: automated matches (15)

Agrobacterium vitis [TaxId: 311402] (2)

1a	d4lb0a_	A:
1b	d4lb0b_	B:

(no "CATH Domain" information available for 4LB0)

(no "Pfam Domain" information available for 4LB0)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:114 - Pro A:115	[ RasMol ]
		Glu A:57 - Pro A:58	[ RasMol ]
		Glu B:114 - Pro B:115	[ RasMol ]
		Glu B:57 - Pro B:58	[ RasMol ]
		Trp A:246 - Pro A:247	[ RasMol ]
		Trp B:246 - Pro B:247	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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