3CKM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE YRAM (LPOA) C-TERMINAL DOMAIN

Authors :   J. Vijayalakshmi, M. A. Saper

Date :   16 Mar 08 (Deposition) - 13 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A

Keywords :   Yram, Periplasmic-Binding Protein, Lipoprotein, Unliganded, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Vijayalakshmi, B. J. Akerley, M. A. Saper
Structure Of Yram, A Protein Essential For Growth Of Haemophilus Influenzae.
Proteins V. 73 204 2008
PubMed-ID: 18412262 | Reference-DOI: 10.1002/PROT.22033

Molecule 1 - YRAM (HI1655)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETBLUE-2
	Expression System Strain	:	ORIGAMI (DE3) PLACI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, UNP RESIDUES 256-573
	Gene	:	YRAM
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	71421
	Strain	:	RD KW20
	Synonym	:	LPOA

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:468 , SER A:469 , GLU A:510 , TYR A:511 , GLN A:512 , HOH A:606 , HOH A:614 , HOH A:623 , HOH A:666 , HOH A:749	BINDING SITE FOR RESIDUE SO4 A 582
2	AC2	SOFTWARE	SER A:467 , PHE A:486 , ASP A:488 , PHE A:492	BINDING SITE FOR RESIDUE BME A 583

Asymmetric/Biological Unit

No.	Residues
1	A:356	-	A:554

Asymmetric/Biological Unit

No.	Residues
1	Gly A:318	-	Pro A:319

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

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

(no "Exon" information available for 3CKM)

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
	(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:318
 aligned with LPOA_HAEIN | P45299 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:318
                                   266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566        
           LPOA_HAEIN   257 SQIGLLLPLSGDGQILGTTIQSGFNDAKGNSTIPVQVFDTSMNSVQDIIAQAKQAGIKTLVGPLLKQNLDVILADPAQIQGMDVLALNATPNSRAIPQLCYYGLSPEDEAESAANKMWNDGVRNPLVAMPQNDLGQRVGNAFNVRWQQLAGTDANIRYYNLPADVTYFVQENNSNTTALYAVASPTELAEMKGYLTNIVPNLAIYASSRASASATNTNTDFIAQMNGVQFSDIPFFKDTNSPQYQKLAKSTGGEYQLMRLYAMGADAWLLINQFNELRQVPGYRLSGLTGILSADTNCNVERDMTWYQYQDGAIVPVA 574
               SCOP domains d3ckma1 A:257-573 YraM C-terminal domain                                                                                                                                                                                                                                                                                     - SCOP domains
               CATH domains 3ckmA01 A:257-360,A:489-561  [code=3.40.50.2300, no name defined]                                       3ckmA02 A:361-488,A:562-574  [code=3.40.50.2300, no name defined]                                                               3ckmA01 A:257-360,A:489-561  [code=3.40.50.2300, no name defined]        3ckmA02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhh..eeee............eee...hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh.....eeee..hhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..eeeee.....eeee.eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ckm A 257 SQIGLLLPLSGDGQILGTTIQSGFNDAKGNSTIPVQVFDTSmNSVQDIIAQAKQAGIKTLVGPLLKQNLDVILADPAQIQGmDVLALNATPNSRAIPQLCYYGLSPEDEAESAANKmWNDGVRNPLVAmPQNDLGQRVGNAFNVRWQQLAGTDANIRYYNLPADVTYFVQENNSNTTALYAVASPTELAEmKGYLTNIVPNLAIYASSRASASATNTNTDFIAQmNGVQFSDIPFFKDTNSPQYQKLAKSTGGEYQLmRLYAmGADAWLLINQFNELRQVPGYRLSGLTGILSADTNCNVERDmTWYQYQDGAIVPVV 574
                                   266       276       286       296 |     306       316       326       336 |     346       356       366      |376       386       396       406       416       426       436       446|      456       466       476    |  486       496       506       516  |    526       536       546       556   |   566        
                                                                   298-MSE                                 338-MSE                            373-MSE     385-MSE                                                       447-MSE                           481-MSE                          514-MSE|                                      560-MSE          
                                                                                                                                                                                                                                                                                                519-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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: L-arabinose binding protein-like (114)

Protein domain: YraM C-terminal domain (1)

Haemophilus influenzae [TaxId: 727] (1)

d3ckma1

A:257-573

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Haemophilus influenzae rd kw20. Organism_taxid: 71421. Strain: rd kw20. (1)

1a	3ckmA02	A:361-488,A:562-574
1b	3ckmA01	A:257-360,A:489-561

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LPOA_HAEIN | P45299)

molecular function
	GO:0030234	enzyme regulator activity	Binds to and modulates the activity of an enzyme.
biological process
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031241	periplasmic side of cell outer membrane	The side (leaflet) of the outer membrane that faces the periplasm of the cell.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Gly A:318 - Pro A:319	[ RasMol ]

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2h4a	REPLACES 2H4A COORDINATES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (7, 7)

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