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- PDB-2l74: Solution structure of the PilZ domain protein PA4608 complex with... -

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Basic information

Entry
Database: PDB / ID: 2l74
TitleSolution structure of the PilZ domain protein PA4608 complex with c-di-GMP identifies charge clustering as molecular readout
ComponentsPutative uncharacterized protein PA4608
Keywordsc-di-GMP binding protein / PilZ / PA4608 / c-di-GMP / Unknown Function
Function / homology
Function and homology information


: / cyclic-di-GMP binding
Similarity search - Function
Cyclic di-GMP binding protein, PA4608 type / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-C2E / Cyclic diguanosine monophosphate-binding protein PA4608
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHabazettl, J. / Allan, M. / Jenal, U. / Grzesiek, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Solution structure of the PilZ domain protein PA4608 complex with cyclic di-GMP identifies charge clustering as molecular readout
Authors: Habazettl, J. / Allan, M.G. / Jenal, U. / Grzesiek, S.
History
DepositionDec 2, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein PA4608
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1463
Polymers16,7651
Non-polymers1,3812
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein PA4608


Mass: 16764.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4608 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HVI1
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP, Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
Nonpolymer detailsTHE NOMENCLATURE OF C2E IN PDB FOLLOWS THE PDB'S CHEMICAL COMPONENT DICTIONARY. THEREFORE ...THE NOMENCLATURE OF C2E IN PDB FOLLOWS THE PDB'S CHEMICAL COMPONENT DICTIONARY. THEREFORE DISCREPANCY OF NOMENCLATURE WILL APPEAR BETWEEN PDB AND THE REFERENCE ARTICLE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1943D (H)CCH-TOCSY (Ribose)
31043D (H)CCH-COSY (Ribose)
1113HAHB
1124HAHB (Ribose)
1135HAHB (Ribose)
114613C-{13Cg}spin-echo difference H-15N HSQC
115615N-{13Cg} spin-echo diference H-15N HAQC
1163Methyl C
1173Methyl N
11863D 1H-15N ROESY
11913D 1H-15N NOESY
12013D 1H-13C NOESY aliphatic
12113D 1H-13C NOESY aromatic
12263D 1H-13C NOESY(Ribose)
12334D 13C-13C NOESY
12412D 1H-1H NOESY
12512D 1H-1H NOESY (filtered against H bound to 13C, 15N)
1261IPAP 1H-15N HSQC
1275IPAP 1H-15N HSQC
1286J-resolved ct 13C-HSQC
1295J-resolved ct 13C-HSQC
13072D H-resolved 15N EXSY
23173D H-15N-15N EXSY
1322IPAP 1H-15N HSQC
1338IPAP 1H-15N HSQC
33472D 1H resolved 15N EXSY
23572D 1H-resolved 15N EXSY
13622D 1H-15N HSQC
137215N Relaxation
138115N Relaxation

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Sample preparation

Details
Solution-IDContentsSolvent system
1250 mM sodium chloride-1; 10 mM TRIS-2; 0.01 % sodium azide-3; 95% H2O/5% D2O95% H2O/5% D2O
2250 mM sodium chloride-4; 10 mM TRIS-5; 0.01 % sodium azide-6; 95% H2O/5% D2O95% H2O/5% D2O
3250 mM sodium chloride-7; 10 mM TRIS-8; 0.01 % sodium azide-9; 100% D2O100% D2O
4250 mM sodium chloride-10; 10 mM TRIS-11; 0.01 % sodium azide-12; 100% D2O100% D2O
5250 mM sodium chloride-13; 10 mM TRIS-14; 0.01 % sodium azide-15, 93% H2O/7% D2O93% H2O/7% D2O
6250 mM sodium chloride-16; 10 mM TRIS-17; 0.01 % sodium azide-18; 95% H2O/5% D2O95% H2O/5% D2O
7250 mM sodium chloride-19; 10 mM TRIS-20; 0.01 % sodium azide-21; 95% H2O/5% D2O95% H2O/5% D2O
8250 mM sodium chloride-22; 10 mM TRIS-23; 0.01 % sodium azide-24; 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
250 mMsodium chloride-11
10 mMTRIS-21
0.01 %sodium azide-31
250 mMsodium chloride-42
10 mMTRIS-52
0.01 %sodium azide-62
250 mMsodium chloride-73
10 mMTRIS-83
0.01 %sodium azide-93
250 mMsodium chloride-104
10 mMTRIS-114
0.01 %sodium azide-124
250 mMsodium chloride-135
10 mMTRIS-145
0.01 %sodium azide-155
250 mMsodium chloride-166
10 mMTRIS-176
0.01 %sodium azide-186
250 mMsodium chloride-197
10 mMTRIS-207
0.01 %sodium azide-217
250 mMsodium chloride-228
10 mMTRIS-238
0.01 %sodium azide-248
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.7 ambient 293 K
26.7 ambient 313 K
36.7 ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DPXBrukerDPX8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
SPARKYGoddardchemical shift assignment
SPARKYGoddardstructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SPARKYGoddardrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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