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- PDB-5gzs: Structure of VC protein -

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Basic information

Entry
Database: PDB / ID: 5gzs
TitleStructure of VC protein
ComponentsGGDEF family protein
KeywordsSIGNALING PROTEIN / the periplasmic portion / CdgH / Vibrio cholerae / diguanylate cyclase
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Bacterial periplasmic substrate-binding proteins / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
ARGININE / GGDEF family protein / GGDEF domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.601 Å
AuthorsXu, M. / Wang, Y.Z. / Yang, X.A. / Xie, W. / Jiang, T.
CitationJournal: Sci Rep / Year: 2017
Title: Structural studies of the periplasmic portion of the diguanylate cyclase CdgH from Vibrio cholerae.
Authors: Xu, M. / Wang, Y.Z. / Yang, X.A. / Jiang, T. / Xie, W.
History
DepositionOct 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3922
Polymers51,2171
Non-polymers1751
Water1,33374
1
A: GGDEF family protein
hetero molecules

A: GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7854
Polymers102,4342
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area3320 Å2
ΔGint-17 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.706, 111.706, 138.647
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-648-

HOH

21A-672-

HOH

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Components

#1: Protein GGDEF family protein / CdgH


Mass: 51217.062 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013200_00600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6Q6V3, UniProt: Q9KT38*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 10% w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97848 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.601→40 Å / Num. obs: 16125 / % possible obs: 99 % / Redundancy: 10.5 % / Net I/σ(I): 28.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.601→40 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.07
RfactorNum. reflection% reflection
Rfree0.2866 813 5.04 %
Rwork0.2194 --
obs0.2229 16115 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 0 74 3570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113562
X-RAY DIFFRACTIONf_angle_d1.3534825
X-RAY DIFFRACTIONf_dihedral_angle_d16.651333
X-RAY DIFFRACTIONf_chiral_restr0.061552
X-RAY DIFFRACTIONf_plane_restr0.005620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6008-2.76370.37361360.27872441X-RAY DIFFRACTION97
2.7637-2.9770.31861280.26282520X-RAY DIFFRACTION100
2.977-3.27650.34761330.25152533X-RAY DIFFRACTION100
3.2765-3.75030.31561460.22692548X-RAY DIFFRACTION100
3.7503-4.72380.25681310.18672578X-RAY DIFFRACTION99
4.7238-39.67290.23261390.19862682X-RAY DIFFRACTION97

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