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- PDB-3klo: Vibrio cholerae VpsT bound to c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 3klo
TitleVibrio cholerae VpsT bound to c-di-GMP
ComponentsTranscriptional regulator VpsT
KeywordsTRANSCRIPTION / REC domain / HTH domain / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / nucleotide binding / positive regulation of DNA-templated transcription
Similarity search - Function
: / VpsT-like, receiver domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...: / VpsT-like, receiver domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / D(-)-TARTARIC ACID / Transcriptional regulator, LuxR family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsKrasteva, P.V. / Navarro, V.A.S. / Sondermann, H.
CitationJournal: Science / Year: 2010
Title: Vibrio cholerae VpsT Regulates Matrix Production and Motility by Directly Sensing Cyclic di-GMP.
Authors: Krasteva, P.V. / Fong, J.C. / Shikuma, N.J. / Beyhan, S. / Navarro, M.V. / Yildiz, F.H. / Sondermann, H.
History
DepositionNov 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator VpsT
B: Transcriptional regulator VpsT
C: Transcriptional regulator VpsT
D: Transcriptional regulator VpsT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,93410
Polymers103,8724
Non-polymers3,0626
Water88349
1
A: Transcriptional regulator VpsT
hetero molecules

B: Transcriptional regulator VpsT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4675
Polymers51,9362
Non-polymers1,5313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z+1/41
Buried area1940 Å2
ΔGint-13 kcal/mol
Surface area23120 Å2
MethodPISA
2
C: Transcriptional regulator VpsT
hetero molecules

D: Transcriptional regulator VpsT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4675
Polymers51,9362
Non-polymers1,5313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.703, 121.703, 208.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Transcriptional regulator VpsT


Mass: 25968.002 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 El Tor / Gene: VCA0952, VC_A0952 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KKZ8
#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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-Cl, 0.8M potassium sodium tartrate tetrahydrate, 3-5% PEG-MME 5000, 8-12% Xylitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 60780 / % possible obs: 97.8 % / Redundancy: 14.5 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 4 / Num. unique all: 6048 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KLN

3kln


Resolution: 2.802→47.862 Å / SU ML: 2.39 / σ(F): 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 3197 5.26 %Random
Rwork0.2459 ---
obs0.2483 60780 82.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.909 Å2 / ksol: 0.324 e/Å3
Refinement stepCycle: LAST / Resolution: 2.802→47.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 204 49 6902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076988
X-RAY DIFFRACTIONf_angle_d1.0499471
X-RAY DIFFRACTIONf_dihedral_angle_d20.4822715
X-RAY DIFFRACTIONf_chiral_restr0.0731046
X-RAY DIFFRACTIONf_plane_restr0.0111163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8021-2.8440.37821230.32662140X-RAY DIFFRACTION71
2.844-2.88840.3831270.31862173X-RAY DIFFRACTION72
2.8884-2.93580.32651210.31972250X-RAY DIFFRACTION74
2.9358-2.98640.38641250.30052252X-RAY DIFFRACTION74
2.9864-3.04070.30011380.29812288X-RAY DIFFRACTION77
3.0407-3.09910.32781370.28392369X-RAY DIFFRACTION78
3.0991-3.16240.30581350.28182422X-RAY DIFFRACTION81
3.1624-3.23110.31761380.27332514X-RAY DIFFRACTION83
3.2311-3.30630.28511380.28662535X-RAY DIFFRACTION84
3.3063-3.38890.28761380.26122574X-RAY DIFFRACTION85
3.3889-3.48050.32821520.25842507X-RAY DIFFRACTION83
3.4805-3.58290.32881290.25162421X-RAY DIFFRACTION80
3.5829-3.69850.32871520.25262785X-RAY DIFFRACTION92
3.6985-3.83070.32921400.21452614X-RAY DIFFRACTION86
3.8307-3.9840.19131300.21292447X-RAY DIFFRACTION81
3.984-4.16520.22391400.19812526X-RAY DIFFRACTION84
4.1652-4.38460.26011490.20432676X-RAY DIFFRACTION88
4.3846-4.65910.30231430.17862655X-RAY DIFFRACTION88
4.6591-5.01850.20341560.1792655X-RAY DIFFRACTION89
5.0185-5.52290.28111450.20162683X-RAY DIFFRACTION88
5.5229-6.32050.30971430.24312693X-RAY DIFFRACTION89
6.3205-7.95730.27931520.24532747X-RAY DIFFRACTION91
7.9573-47.86910.25821460.2662657X-RAY DIFFRACTION88

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