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- PDB-5htl: Structure of MshE with cdg -

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Basic information

Entry
Database: PDB / ID: 5htl
TitleStructure of MshE with cdg
ComponentsMSHA biogenesis protein MshE
KeywordsBIOSYNTHETIC PROTEIN / MshE / c-di-GMP
Function / homology
Function and homology information


pilus assembly / : / ATP binding
Similarity search - Function
Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-C2E / MSHA biogenesis protein MshE / MSHA biogenesis protein MshE
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.371 Å
AuthorsChin, K.H. / Wang, Y.C.
CitationJournal: Nat Commun / Year: 2016
Title: Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain.
Authors: Wang, Y.C. / Chin, K.H. / Tu, Z.L. / He, J. / Jones, C.J. / Sanchez, D.Z. / Yildiz, F.H. / Galperin, M.Y. / Chou, S.H.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MSHA biogenesis protein MshE
B: MSHA biogenesis protein MshE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9644
Polymers32,5832
Non-polymers1,3812
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-2 kcal/mol
Surface area14250 Å2
Unit cell
Length a, b, c (Å)52.852, 61.862, 75.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MSHA biogenesis protein MshE


Mass: 16291.353 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsE_3, ERS013202_01172 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: A0A0H6MG30, UniProt: Q9KUV7*PLUS
#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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris 100mM pH 8.0, PEG 3350 20%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97902 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 234156 / % possible obs: 95.4 % / Redundancy: 4.6 % / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.371→26.426 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2211 1943 4 %
Rwork0.2014 --
obs0.2025 48521 92.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 53.696 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5494 Å20 Å20 Å2
2--3.6704 Å20 Å2
3---2.7568 Å2
Refinement stepCycle: LAST / Resolution: 1.371→26.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 92 356 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062337
X-RAY DIFFRACTIONf_angle_d1.2663188
X-RAY DIFFRACTIONf_dihedral_angle_d15.586874
X-RAY DIFFRACTIONf_chiral_restr0.082369
X-RAY DIFFRACTIONf_plane_restr0.005404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.371-1.40520.34861330.30313122X-RAY DIFFRACTION88
1.4052-1.44320.30751390.2883161X-RAY DIFFRACTION89
1.4432-1.48570.31981350.2593267X-RAY DIFFRACTION92
1.4857-1.53370.30991390.23823348X-RAY DIFFRACTION94
1.5337-1.58850.28971430.22413376X-RAY DIFFRACTION95
1.5885-1.6520.2541390.21593438X-RAY DIFFRACTION96
1.652-1.72720.221430.20973425X-RAY DIFFRACTION96
1.7272-1.81830.24141430.20373441X-RAY DIFFRACTION95
1.8183-1.93220.2241440.19613454X-RAY DIFFRACTION96
1.9322-2.08130.22171430.18923429X-RAY DIFFRACTION95
2.0813-2.29060.21591400.17923407X-RAY DIFFRACTION94
2.2906-2.62180.19551400.19453399X-RAY DIFFRACTION93
2.6218-3.30220.20821420.18833412X-RAY DIFFRACTION93
3.3022-26.43090.23661200.19852899X-RAY DIFFRACTION76
Refinement TLS params.Method: refined / Origin x: -0.9985 Å / Origin y: -6.2351 Å / Origin z: 2.0627 Å
111213212223313233
T0.1034 Å20.0105 Å2-0.0086 Å2-0.1073 Å20.0019 Å2--0.1086 Å2
L0.2352 °20.1388 °2-0.065 °2-0.3387 °20.0259 °2--0.2557 °2
S0.0212 Å °0.0055 Å °-0.01 Å °0.0108 Å °-0.002 Å °-0.0126 Å °0.0062 Å °0.0082 Å °0 Å °
Refinement TLS groupSelection details: all

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