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- PDB-3kln: Vibrio cholerae VpsT -

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Basic information

Entry
Database: PDB / ID: 3kln
TitleVibrio cholerae VpsT
ComponentsTranscriptional regulator, LuxR family
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
Transcriptional regulator, LuxR family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.078 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 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, LuxR family
B: Transcriptional regulator, LuxR family
C: Transcriptional regulator, LuxR family
D: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)103,8724
Polymers103,8724
Non-polymers00
Water00
1
A: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)25,9681
Polymers25,9681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)25,9681
Polymers25,9681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)25,9681
Polymers25,9681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)25,9681
Polymers25,9681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Transcriptional regulator, LuxR family

B: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)51,9362
Polymers51,9362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area21780 Å2
MethodPISA
6
C: Transcriptional regulator, LuxR family

D: Transcriptional regulator, LuxR family


Theoretical massNumber of molelcules
Total (without water)51,9362
Polymers51,9362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z+1/41
Buried area1750 Å2
ΔGint-11 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.489, 121.489, 198.290
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, LuxR family


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

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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: 3.52 Å3/Da / Density % sol: 65.08 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9788
SYNCHROTRONNSLS X29A20.9794
SYNCHROTRONNSLS X29A31.0809
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97941
31.08091
ReflectionResolution: 3.078→50 Å / Num. all: 52740 / Num. obs: 52138 / % possible obs: 99.2 % / Redundancy: 10 % / Net I/σ(I): 11.8
Reflection shellResolution: 3.078→3.27 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 8187 / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.078→45.899 Å / SU ML: 2.41 / σ(F): 1.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3083 2589 5 %Random
Rwork0.2475 ---
obs0.2505 51824 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.326 Å2 / ksol: 0.331 e/Å3
Refinement stepCycle: LAST / Resolution: 3.078→45.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 0 0 6640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116753
X-RAY DIFFRACTIONf_angle_d1.2719107
X-RAY DIFFRACTIONf_dihedral_angle_d19.9142551
X-RAY DIFFRACTIONf_chiral_restr0.0821045
X-RAY DIFFRACTIONf_plane_restr0.0041141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0779-3.13710.38551330.39892511X-RAY DIFFRACTION91
3.1371-3.20110.38721440.35132806X-RAY DIFFRACTION99
3.2011-3.27070.34221430.31262724X-RAY DIFFRACTION100
3.2707-3.34670.35071490.32282752X-RAY DIFFRACTION99
3.3467-3.43040.33611430.30232771X-RAY DIFFRACTION99
3.4304-3.52310.32841450.27692749X-RAY DIFFRACTION99
3.5231-3.62680.31851440.25332741X-RAY DIFFRACTION99
3.6268-3.74380.30791460.24632772X-RAY DIFFRACTION99
3.7438-3.87750.26611480.23442765X-RAY DIFFRACTION100
3.8775-4.03270.30091500.23982732X-RAY DIFFRACTION99
4.0327-4.21610.32181500.222781X-RAY DIFFRACTION99
4.2161-4.43820.26221380.20882723X-RAY DIFFRACTION99
4.4382-4.7160.24191460.19682767X-RAY DIFFRACTION99
4.716-5.07970.29361360.21022765X-RAY DIFFRACTION99
5.0797-5.59010.34561460.20732767X-RAY DIFFRACTION100
5.5901-6.39710.25521450.23372770X-RAY DIFFRACTION100
6.3971-8.05260.29941450.21822739X-RAY DIFFRACTION99
8.0526-45.90360.30961380.24432600X-RAY DIFFRACTION93

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