3N8U - JenaLib

Title :   CRYSTAL STRUCTURE OF AN IMELYSIN PEPTIDASE (BACOVA_03801) FROM BACTEROIDES OVATUS AT 1.44 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   28 May 10 (Deposition) - 28 Jul 10 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.44

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

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Xu, N. D. Rawlings, C. L. Farr, H. J. Chiu, J. C. Grant, L. Jaroszewski H. E. Klock, M. W. Knuth, M. D. Miller, D. Weekes, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structural And Sequence Analysis Of Imelysin-Like Proteins Implicated In Bacterial Iron Uptake.
Plos One V. 6 21875 2011
PubMed-ID: 21799754 | Reference-DOI: 10.1371/JOURNAL.PONE.0021875

Compounds

Molecule 1 - IMELYSIN PEPTIDASE
	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	:	BACOVA_03801
	Organism Scientific	:	BACTEROIDES OVATUS
	Organism Taxid	:	411476
	Strain	:	ATCC 8483

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 20)

Asymmetric Unit (4, 20)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
3	MG	3	Ligand/Ion	MAGNESIUM ION
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:111 , HOH A:527 , HOH A:543 , HOH A:572 , HOH A:578 , HOH A:620 , HOH A:662	BINDING SITE FOR RESIDUE MG A 1
02	AC2	SOFTWARE	HOH A:570 , HOH A:876 , HOH A:1179 , HOH B:416 , HOH B:526 , HOH B:536	BINDING SITE FOR RESIDUE MG A 2
03	AC3	SOFTWARE	TRP A:142 , SER A:144 , PRO A:204 , ARG A:206 , HOH A:524	BINDING SITE FOR RESIDUE CL A 5
04	AC4	SOFTWARE	PRO A:329 , LEU A:330 , ASP A:331 , ASN A:363	BINDING SITE FOR RESIDUE EDO A 7
05	AC5	SOFTWARE	ASN A:110 , THR A:114 , GLY A:118 , ASP A:119 , ASN A:122 , GLU A:225 , LYS A:229 , HOH A:656 , HOH A:665 , HOH A:759 , HOH A:828	BINDING SITE FOR RESIDUE EDO A 12
06	AC6	SOFTWARE	HOH B:426 , HOH B:466 , HOH B:483 , HOH B:495 , HOH B:516 , HOH B:556	BINDING SITE FOR RESIDUE MG B 3
07	AC7	SOFTWARE	TRP B:142 , SER B:144 , ARG B:206	BINDING SITE FOR RESIDUE CL B 4
08	AC8	SOFTWARE	LYS B:104 , GLU B:107 , ASP B:317 , HOH B:851 , HOH B:1104	BINDING SITE FOR RESIDUE EDO B 6
09	AC9	SOFTWARE	SER B:72 , GLY B:75 , GLY B:76 , HOH B:661 , HOH B:676 , HOH B:722	BINDING SITE FOR RESIDUE EDO B 8
10	BC1	SOFTWARE	THR B:264 , GLU B:303 , LYS B:307 , HOH B:544	BINDING SITE FOR RESIDUE EDO B 9
11	BC2	SOFTWARE	ASN B:150 , GLN B:199	BINDING SITE FOR RESIDUE EDO B 10
12	BC3	SOFTWARE	GLN B:203 , PRO B:204 , ASN B:207	BINDING SITE FOR RESIDUE EDO B 11

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:352
 aligned with A7M120_BACO1 | A7M120 from UniProtKB/TrEMBL  Length:384

    Alignment length:352
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382  
         A7M120_BACO1    33 DPANIDYTPENASSWHNYMRNVAALLKTDATNLYNAWNSSYKGGESYASLFKAHSGSPYASALSCVEEIVDKCAEIANEVGTAKIGDPYNLYKAGNTEEALYAVESWYSWHSRDDYTNNIYSIRNAYYGSLDGNINANSLSTVIAGANSSLDTKIKNAIQKAAKAIQDIPQPFRNHIPSNETVAAMDACAELESILKNDLKSYIANNSNNINTDAVLNPVVTQYVDAVVVPTYKSLKEKNDALYNAVIVLADNPSNSAFETACDAWITAREPWEKSEAFLFGPVDEMGLDPNMDSWPLDQNAIVQILNSQSWSDLEWSEGDDEAAVESAQNVRGFHTLEFLLYKNGEPRKVQ 384
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhee..ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n8u A  33 DPANIDYTPENASSWHNYmRNVAALLKTDATNLYNAWNSSYKGGESYASLFKAHSGSPYASALSCVEEIVDKCAEIANEVGTAKIGDPYNLYKAGNTEEALYAVESWYSWHSRDDYTNNIYSIRNAYYGSLDGNINANSLSTVIAGANSSLDTKIKNAIQKAAKAIQDIPQPFRNHIPSNETVAAmDACAELESILKNDLKSYIANNSNNINTDAVLNPVVTQYVDAVVVPTYKSLKEKNDALYNAVIVLADNPSNSAFETACDAWITAREPWEKSEAFLFGPVDEmGLDPNmDSWPLDQNAIVQILNSQSWSDLEWSEGDDEAAVESAQNVRGFHTLEFLLYKNGEPRKVQ 384
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     | 222       232       242       252       262       272       282       292       302       312      |322  |    332       342       352       362       372       382  
                                             51-MSE                                                                                                                                                                218-MSE                                                                                              319-MSE |                                                           
                                                                                                                                                                                                                                                                                                                              325-MSE

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with A7M120_BACO1 | A7M120 from UniProtKB/TrEMBL  Length:384

    Alignment length:354
                                    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       330       340       350       360       370       380    
         A7M120_BACO1    31 TVDPANIDYTPENASSWHNYMRNVAALLKTDATNLYNAWNSSYKGGESYASLFKAHSGSPYASALSCVEEIVDKCAEIANEVGTAKIGDPYNLYKAGNTEEALYAVESWYSWHSRDDYTNNIYSIRNAYYGSLDGNINANSLSTVIAGANSSLDTKIKNAIQKAAKAIQDIPQPFRNHIPSNETVAAMDACAELESILKNDLKSYIANNSNNINTDAVLNPVVTQYVDAVVVPTYKSLKEKNDALYNAVIVLADNPSNSAFETACDAWITAREPWEKSEAFLFGPVDEMGLDPNMDSWPLDQNAIVQILNSQSWSDLEWSEGDDEAAVESAQNVRGFHTLEFLLYKNGEPRKVQ 384
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n8u B  31 TVDPANIDYTPENASSWHNYmRNVAALLKTDATNLYNAWNSSYKGGESYASLFKAHSGSPYASALSCVEEIVDKCAEIANEVGTAKIGDPYNLYKAGNTEEALYAVESWYSWHSRDDYTNNIYSIRNAYYGSLDGNINANSLSTVIAGANSSLDTKIKNAIQKAAKAIQDIPQPFRNHIPSNETVAAmDACAELESILKNDLKSYIANNSNNINTDAVLNPVVTQYVDAVVVPTYKSLKEKNDALYNAVIVLADNPSNSAFETACDAWITAREPWEKSEAFLFGPVDEmGLDPNmDSWPLDQNAIVQILNSQSWSDLEWSEGDDEAAVESAQNVRGFHTLEFLLYKNGEPRKVQ 384
                                    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    |  330       340       350       360       370       380    
                                               51-MSE                                                                                                                                                                218-MSE                                                                                              319-MSE |                                                           
                                                                                                                                                                                                                                                                                                                                325-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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:203 - Pro A:204	[ RasMol ]
		Gln B:203 - Pro B:204	[ RasMol ]
		Ser A:89 - Pro A:90	[ RasMol ]
		Ser B:89 - Pro B:90	[ RasMol ]
		Trp A:328 - Pro A:329	[ RasMol ]
		Trp B:328 - Pro B:329	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3n8u
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A7M120_BACO1 \| A7M120
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	A7M120_BACO1 \| A7M120
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description