4KVS - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PROCHLOROCOCCUS MARINUS ALDEHYDE-DEFORMYLATING OXYGENASE (MUTANT A134F)

Authors :   C. W. Levy, B. Khara, N. Menon, D. Mansell, D. Das, E. N. G. Marsh, D. Leys, N. S. Scrutton

Date :   23 May 13 (Deposition) - 26 Jun 13 (Release) - 28 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

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

Keywords :   Propane Production, Aldehyde-Deformylating Oxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Khara, N. Menon, C. Levy, D. Mansell, D. Das, E. N. Marsh, D. Leys, N. S. Scrutton
Production Of Propane And Other Short-Chain Alkanes By Structure-Based Engineering Of Ligand Specificity In Aldehyde-Deformylating Oxygenase.
Chembiochem V. 14 1204 2013
PubMed-ID: 23757044 | Reference-DOI: 10.1002/CBIC.201300307

Molecule 1 - ALDEHYDE DECARBONYLASE
	Chains	:	A
	EC Number	:	4.1.99.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Gene	:	PMT_1231
	Mutation	:	YES
	Organism Scientific	:	PROCHLOROCOCCUS MARINUS
	Organism Taxid	:	74547
	Strain	:	MIT 9313
	Synonym	:	AD, FATTY ALDEHYDE DECARBONYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	6NA	1	Ligand/Ion	HEXANOIC ACID
2	FE	2	Ligand/Ion	FE (III) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	6NA	1	Ligand/Ion	HEXANOIC ACID
2	FE	-1	Ligand/Ion	FE (III) ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	6NA	2	Ligand/Ion	HEXANOIC ACID
2	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:44 , GLU A:45 , ALA A:48 , GLU A:73 , GLN A:123 , ILE A:127 , GLU A:128 , ALA A:131 , GLU A:157 , FE A:302 , FE A:303	BINDING SITE FOR RESIDUE 6NA A 301
2	AC2	SOFTWARE	GLU A:45 , GLU A:73 , HIS A:76 , GLU A:157 , 6NA A:301 , FE A:303	BINDING SITE FOR RESIDUE FE A 302
3	AC3	SOFTWARE	GLU A:73 , GLU A:128 , GLU A:157 , HIS A:160 , 6NA A:301 , FE A:302	BINDING SITE FOR RESIDUE FE A 303

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

(no "Cis Peptide Bond" information available for 4KVS)

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

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

(no "Exon" information available for 4KVS)

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:221
                                                                                                                                                                                                                                                             
               SCOP domains d4kvsa_ A: Hypothetical protein PMT1231                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvs A  21 ALPDFTSDRYKDAYSRINAIVIEGEQEAHDNYIAIGTLLPDHVEELKRLAKMEMRHKKGFTACGKNLGVEADMDFAREFFAPLRDNFQTALGQGKTPTCLLIQALLIEAFAISFYHTYIPVSDPFARKITEGVVKDEYTHLNYGEAWLKANLESCREELLEANRENLPLIRRMLDQVAGDAAVLQMDKEDLIEDFLIAYQESLTEIGFNTREITRMAAAAL 241
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: PMT1231-like (4)

Protein domain: Hypothetical protein PMT1231 (4)

Prochlorococcus marinus [TaxId: 1219] (4)

d4kvsa_

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

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

Asymmetric Unit(hide GO term definitions)

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
		6NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4kvs)

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

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)

Access by PDB/NDB ID
	4kvs
		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
	ALDEC_PROMM \| Q7V6D4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.1.99.5
		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

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
	ALDEC_PROMM \| Q7V6D4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ALDEC_PROMM \| Q7V6D4	:	2oc5 4kvq 4kvr 4pg0 4pg1 4pgi 4pgk 4tw3

2oc5	CRYSTAL STRUCTURE OF A FERRITIN-LIKE PROTEIN (PMT1231) FROM PROCHLOROCOCCUS MARINUS STR. MIT 9313 AT 1.68 A RESOLUTION
4kvq	CRYSTAL STRUCTURE OF PROCHLOROCOCCUS MARINUS ALDEHYDE- DEFORMYLATING OXYGENASE WILD TYPE WITH PALMITIC ACID BOUND
4kvr	CRYSTAL STRUCTURE OF PROCHLOROCOCCUS MARINUS ALDEHYDE- DEFORMYLATING OXYGENASE (MUTANT V41Y)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File