3BS6 - JenaLib

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Title :   1.8 ANGSTROM CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF THE MEMBRANE INSERTASE YIDC

Authors :   S. Ravaud, I. Sinning

Date :   22 Dec 07 (Deposition) - 12 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Yidc/Oxa1/Alb3 Family, Membrane Insertion, Chaperone, Sec Translocon, Periplasmic Domain, Beta Supersandwich Fold, Helical Linker Domain, Membrane Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ravaud, G. Stjepanovic, K. Wild, I. Sinning
The Crystal Structure Of The Periplasmic Domain Of The Escherichia Coli Membrane Protein Insertase Yidc Contains A Substrate Binding Cleft
J. Biol. Chem. V. 283 9350 2008
PubMed-ID: 18234665 | Reference-DOI: 10.1074/JBC.M710493200
(for further references see the PDB file header)

Molecule 1 - INNER MEMBRANE PROTEIN OXAA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24D
	Expression System Strain	:	BL21 PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 56-329
	Gene	:	OXAA, YIDC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PERIPLASMIC DOMAIN OF YIDC (P1D)

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 25)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CA	5	Ligand/Ion	CALCIUM ION
3	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	3	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	2PE	-1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (4, 10)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 3 (4, 20)

No.	Name	Count	Type	Full Name
1	2PE	-1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:230 , GLU A:231 , HOH A:343 , HOH A:354 , GLU B:228 , TYR B:230 , GLU B:231	BINDING SITE FOR RESIDUE CA A 1
02	AC2	SOFTWARE	GLU A:231 , HOH A:485 , GLU B:228 , GLU B:231 , HOH B:516	BINDING SITE FOR RESIDUE CA A 2
03	AC3	SOFTWARE	GLU A:228 , GLU B:231 , LYS B:232 , HOH B:416 , HOH B:589	BINDING SITE FOR RESIDUE CA A 3
04	AC4	SOFTWARE	ASN A:125 , HOH A:476 , ALA B:124 , HOH B:392	BINDING SITE FOR RESIDUE CA A 4
05	AC5	SOFTWARE	ALA A:124 , HOH A:370 , HOH A:378 , ASN B:125	BINDING SITE FOR RESIDUE CA A 5
06	AC6	SOFTWARE	PHE A:193 , GLN A:195 , ASN A:273 , LYS A:289 , 2PE B:1	BINDING SITE FOR RESIDUE PG4 A 336
07	AC7	SOFTWARE	HIS A:267 , THR A:300 , GLY A:301 , ALA A:302 , MSE A:303 , ASN A:304 , EDO A:340 , HOH A:382 , HOH A:496 , HOH A:515 , HOH A:539 , GLY B:143 , ASN B:145	BINDING SITE FOR RESIDUE PGE A 337
08	AC8	SOFTWARE	GLU A:146 , GLN A:148 , ASN A:177 , ASN A:304 , HOH A:453 , HOH A:465 , HOH A:508 , ASN B:145 , GLU B:146 , LYS B:168 , ARG B:169 , HOH B:518	BINDING SITE FOR RESIDUE PGE A 338
09	AC9	SOFTWARE	LYS A:64 , HOH A:510	BINDING SITE FOR RESIDUE EDO A 339
10	BC1	SOFTWARE	SER A:192 , ASN A:268 , SER A:290 , MSE A:303 , ASN A:304 , PGE A:337 , HOH A:515 , HOH A:555	BINDING SITE FOR RESIDUE EDO A 340
11	BC2	SOFTWARE	ASP A:315 , HOH A:361 , HOH A:520	BINDING SITE FOR RESIDUE EDO A 7
12	BC3	SOFTWARE	PG4 A:336 , GLN B:111 , ARG B:128 , PHE B:193 , ASN B:245 , THR B:271 , ASN B:273 , TYR B:275 , LYS B:289 , SER B:290 , GLN B:291 , HOH B:549 , HOH B:587 , HOH B:614	BINDING SITE FOR RESIDUE 2PE B 1
13	BC4	SOFTWARE	ASN B:132 , GLU B:134 , TYR B:138 , PRO B:150 , HOH B:608	BINDING SITE FOR RESIDUE PGE B 336
14	BC5	SOFTWARE	TYR B:87 , ILE B:313	BINDING SITE FOR RESIDUE EDO B 337
15	BC6	SOFTWARE	LYS B:64 , VAL B:139 , HOH B:548	BINDING SITE FOR RESIDUE EDO B 3
16	BC7	SOFTWARE	ASP B:136	BINDING SITE FOR RESIDUE EDO B 4
17	BC8	SOFTWARE	ALA B:86 , TYR B:87 , HOH B:611	BINDING SITE FOR RESIDUE EDO B 6

(no "SS Bond" information available for 3BS6)

(no "Cis Peptide Bond" information available for 3BS6)

(no "SAP(SNP)/Variant" information available for 3BS6)

(no "PROSITE Motif" information available for 3BS6)

(no "Exon" information available for 3BS6)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:258
 aligned with YIDC_ECOLI | P25714 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:271
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 
           YIDC_ECOLI    59 KLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVD 329
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeee....eeeeeeeeeee.......eeeeeeee..eeeeeeeeee......hhhhh..........eee......eeeeeeeee.....eeeeeeeee....eeeeeeeee......eeeeeeeeeeee....-------------...eeeee......eeehhhhhhh....eeeee..eeeeee..eeeeeeee...eeeeeeeeee..eeeeeee...eee....eeeeeeeeeee..hhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bs6 A  59 KLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPmTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLP-------------TFRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAmLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAmNSTLWVGPEIQDKmAAVAPHLDLTVD 329
                                    68        78        88        98       108       118       128       138       148  |    158       168       178       188       198    |    -       218       228       238       248      |258       268       278       288       298    |  308       318       328 
                                                                                                                      151-MSE                                             203           217                                   255-MSE                                         303-MSE       317-MSE

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with YIDC_ECOLI | P25714 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:275
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325     
           YIDC_ECOLI    56 GQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVDY 330
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeee....eeeeeeeeeee.......eee..eee..eeeeeeeeee......hhhhh..........eee......eeeeeeeee.....eeeeeeeee....eeeeeeeee......eeeeeeeeeeee...---------------..eeeee......eeehhhhhhh....eeeee..eeeeee..eeeeeeee...eeeeeeeeee..eeeeeee...eee....eeeeeeeeeeee.hhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bs6 B  56 GQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPmTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITL---------------FRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAmLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAmNSTLWVGPEIQDKmAAVAPHLDLTVDH 330
                                    65        75        85        95       105       115       125       135       145     | 155       165       175       185       195      |  -         -  |    225       235       245       255       265       275       285       295       305       315 |     325     
                                                                                                                         151-MSE                                            202             218                                  255-MSE                                         303-MSE       317-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 3BS6)

(no "CATH Domain" information available for 3BS6)

(no "Pfam Domain" information available for 3BS6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (YIDC_ECOLI | P25714)

molecular function
	GO:0032977	membrane insertase activity	Mediates the integration of proteins into a membrane from the inner side of the membrane. Membrane insertases are highly conserved and include the bacterial YidC family, the plant chloroplast Alb3 family, and the fungal and animal mitochondrial Oxa1/Cox18 family.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0051205	protein insertion into membrane	The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Cis Peptide Bonds
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	3bs6
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Description

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Ligands, Modified Residues, Ions (6, 25)

Sites (17, 17)

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