2R6O - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE FROM THIOBACILLUS DENITRIFICANS

Authors :   C. Chang, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak, Mi Center For Structural Genomics (Mcsg)

Date :   06 Sep 07 (Deposition) - 18 Sep 07 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Diguanylate Cyclase, Ggdef And Eal Domains, Thiobacillus Denitrificans, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Tchigvintsev, X. Xu, A. Singer, C. Chang, G. Brown, M. Proudfoot, H. Cui, R. Flick, W. F. Anderson, A. Joachimiak, M. Y. Galperin, A. Savchenko, A. F. Yakunin
Structural Insight Into The Mechanism Of C-Di-Gmp Hydrolysi By Eal Domain Phosphodiesterases.
J. Mol. Biol. V. 402 524 2010
PubMed-ID: 20691189 | Reference-DOI: 10.1016/J.JMB.2010.07.050

Molecule 1 - PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE (GGDEF & EAL DOMAINS)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET DERIVATIVE
	Expression System Strain	:	BL21(DE3) DERIVATIVE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 487-758
	Gene	:	TBD_1265
	Organism Scientific	:	THIOBACILLUS DENITRIFICANS
	Organism Taxid	:	292415
	Strain	:	ATCC 25259

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1 , HOH A:12 , GLU A:523 , ASN A:584 , GLU A:616 , ASP A:646	BINDING SITE FOR RESIDUE MG A 801
2	AC2	SOFTWARE	HOH B:9 , HOH B:11 , GLU B:523 , ASN B:584 , GLU B:616 , ASP B:646	BINDING SITE FOR RESIDUE MG B 802
3	AC3	SOFTWARE	HOH B:34 , HOH B:139 , HOH B:229 , HOH B:378 , ASP B:647 , ASP B:669	BINDING SITE FOR RESIDUE MG B 803
4	AC4	SOFTWARE	VAL A:526 , ASN A:584	BINDING SITE FOR RESIDUE CL A 804
5	AC5	SOFTWARE	HOH A:369 , PRO A:538 , SER A:539 , ARG A:567	BINDING SITE FOR RESIDUE CL A 805
6	AC6	SOFTWARE	MSE A:537 , ARG A:609	BINDING SITE FOR RESIDUE CL A 806

(no "SS Bond" information available for 2R6O)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:676	-	Pro A:677
2	Ile B:676	-	Pro B:677

(no "SAP(SNP)/Variant" information available for 2R6O)

(no "PROSITE Motif" information available for 2R6O)

(no "Exon" information available for 2R6O)

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:258
 aligned with Q3SJE6_THIDA | Q3SJE6 from UniProtKB/TrEMBL  Length:758

    Alignment length:258
                                   497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737        
         Q3SJE6_THIDA   488 RLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVMPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVMLVMTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADAFASLLDRQKA 745
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r6oA00 A:488-745 EAL domain-like                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeehhhhhh....hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...ee........eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r6o A 488 RLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVmPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVmLVmTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGmEVVAEGIETAQQYAFLRDRGCEFGQGNLmSTPQAADAFASLLDRQKA 745
                                   497       507       517       527       537       547       557       567       577       587       597       607       617    |  627       637       647       657       667       677       687       697|      707       717       727       737        
                                                                           537-MSE                                                                              622-MSE                                                                     698-MSE                      727-MSE              
                                                                                                                                                                   625-MSE

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with Q3SJE6_THIDA | Q3SJE6 from UniProtKB/TrEMBL  Length:758

    Alignment length:258
                                   498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738        
         Q3SJE6_THIDA   489 LTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVMPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVMLVMTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADAFASLLDRQKAS 746
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2r6oB00 B:489-746 EAL domain-like                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ---EAL-2r6oB01 B:492-730                                                                                                                                                                                                                          ---------------- Pfam domains (1)
           Pfam domains (2) ---EAL-2r6oB02 B:492-730                                                                                                                                                                                                                          ---------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeeeee..----------------hhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhh.hhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhh...eeeehhhhhh....hhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhh....ee........eehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r6o B 489 LTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWED----------------DTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVmLVmTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGmEVVAEGIETAQQYAFLRDRGCEFGQGNLmSTPQAADAFASLLDRQKAS 746
                                   498       508       518       528 |       -       548       558       568       578       588       598       608       618   |  |628       638       648       658       668       678       688       698       708       718       728       738        
                                                                   530              547                                                                        622-MSE                                                                     698-MSE                      727-MSE               
                                                                                                                                                                  625-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 2R6O)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: EAL domain-like (4)

Thiobacillus denitrificans atcc 25259. Organism_taxid: 292415. Strain:atcc 25259. (2)

1a	2r6oB00	B:489-746
1b	2r6oA00	A:488-745

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: EAL] (10)

Family: EAL (10)

Thiobacillus denitrificans (strain ATCC 25259) (2)

1a	EAL-2r6oB01	B:492-730
1b	EAL-2r6oB02	B:492-730

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q3SJE6_THIDA | Q3SJE6)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ile A:676 - Pro A:677	[ RasMol ]
		Ile B:676 - Pro B:677	[ RasMol ]

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	2r6o
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(no "Related Entries Specified in the PDB File" available for 2R6O)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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