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- PDB-3iwz: The c-di-GMP Responsive Global Regulator CLP Links Cell-Cell Sign... -

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Basic information

Entry
Database: PDB / ID: 3iwz
TitleThe c-di-GMP Responsive Global Regulator CLP Links Cell-Cell Signaling to Virulence Gene Expression in Xanthomonas campestris
ComponentsCatabolite activation-like protein
KeywordsTRANSCRIPTION / Xcc / pathogenicity / CRP / CLP / c-di-GMP receptor / Quorum Sensing / DNA-binding / Transcription regulation
Function / homology
Function and homology information


cyclic-di-GMP binding / : / metabolic process / catalytic activity / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Bacterial regulatory proteins, crp family / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Bacterial regulatory proteins, crp family / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CRP-like protein Clp
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsChin, K.H. / Tu, Z.L. / Tseng, Y.H. / Dow, J.M. / Wang, A.H.J. / Chou, S.H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris.
Authors: Chin, K.H. / Lee, Y.C. / Tu, Z.L. / Chen, C.H. / Tseng, Y.H. / Yang, J.M. / Ryan, R.P. / McCarthy, Y. / Dow, J.M. / Wang, A.H. / Chou, S.H.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catabolite activation-like protein
B: Catabolite activation-like protein
C: Catabolite activation-like protein
D: Catabolite activation-like protein


Theoretical massNumber of molelcules
Total (without water)102,9904
Polymers102,9904
Non-polymers00
Water5,026279
1
A: Catabolite activation-like protein
D: Catabolite activation-like protein


Theoretical massNumber of molelcules
Total (without water)51,4952
Polymers51,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-32 kcal/mol
Surface area19800 Å2
MethodPISA
2
B: Catabolite activation-like protein
C: Catabolite activation-like protein


Theoretical massNumber of molelcules
Total (without water)51,4952
Polymers51,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-32 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.690, 67.690, 110.370
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Catabolite activation-like protein / CAP-like


Mass: 25747.377 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P22260
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris 8.5, PEG 3350 20%, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97966 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97966 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42637 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 24.5
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→29.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 215908.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.305 4049 10.1 %RANDOM
Rwork0.244 ---
obs0.244 40040 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6187 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å20 Å2-7.65 Å2
2--0.89 Å20 Å2
3---2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 0 279 6817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 604 9.5 %
Rwork0.264 5774 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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