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- PDB-5z7c: crystal structure of cyclic GMP-AMP specifc phosphodiesterases in... -

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Basic information

Entry
Database: PDB / ID: 5z7c
Titlecrystal structure of cyclic GMP-AMP specifc phosphodiesterases in V.cholerae (V-cGAP3)
Components3'3'-cGAMP-specific phosphodiesterase 3
KeywordsMETAL BINDING PROTEIN / Cyclic dinucleotides / phosphodiesterase.
Function / homology
Function and homology information


cyclic-nucleotide phosphodiesterase activity / cyclic nucleotide catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / metal ion binding
Similarity search - Function
HD domain / HD-GYP domain / HD-GYP domain profile. / HD domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
3'3'-cGAMP-specific phosphodiesterase 3
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.76 Å
AuthorsDeng, M.J. / Ye, Z.Y. / Su, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670740 and U1430237 China
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Novel Mechanism for Cyclic Dinucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3.
Authors: Deng, M.J. / Tao, J. / E, C. / Ye, Z.Y. / Jiang, Z. / Yu, J. / Su, X.D.
History
DepositionJan 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3'3'-cGAMP-specific phosphodiesterase 3


Theoretical massNumber of molelcules
Total (without water)51,5651
Polymers51,5651
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20870 Å2
Unit cell
Length a, b, c (Å)139.360, 139.360, 179.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein 3'3'-cGAMP-specific phosphodiesterase 3 / V-cGAP3


Mass: 51564.652 Da / Num. of mol.: 1 / Mutation: K440A/K441A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_A0931
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9KL18, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 4.87 Å3/Da / Density % sol: 74.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.2M ammonium citrate tribasic, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 26853 / % possible obs: 99.2 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.85
Reflection shellResolution: 2.76→2.9 Å / Rmerge(I) obs: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.76→28.595 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 1352 5.04 %
Rwork0.2465 --
obs0.2475 26848 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→28.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 0 20 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0273283
X-RAY DIFFRACTIONf_angle_d1.6824453
X-RAY DIFFRACTIONf_dihedral_angle_d17.4461206
X-RAY DIFFRACTIONf_chiral_restr0.128512
X-RAY DIFFRACTIONf_plane_restr0.02577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.85860.37211170.35332534X-RAY DIFFRACTION100
2.8586-2.97290.2921330.32622507X-RAY DIFFRACTION100
2.9729-3.10810.33041530.30962500X-RAY DIFFRACTION100
3.1081-3.27170.30551320.29612517X-RAY DIFFRACTION100
3.2717-3.47640.30451280.28992527X-RAY DIFFRACTION100
3.4764-3.74430.25641340.2552533X-RAY DIFFRACTION100
3.7443-4.12010.26331290.22612565X-RAY DIFFRACTION100
4.1201-4.71390.23611460.21152566X-RAY DIFFRACTION100
4.7139-5.93040.25981450.24632597X-RAY DIFFRACTION99
5.9304-28.59630.25571350.22432650X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 53.9313 Å / Origin y: 49.4692 Å / Origin z: 107.9062 Å
111213212223313233
T0.3134 Å20.1145 Å20.0057 Å2-0.4846 Å20.0061 Å2--0.4376 Å2
L0.8828 °2-0.4408 °20.1887 °2-1.7376 °2-0.3446 °2--3.0665 °2
S0.0708 Å °0.0956 Å °-0.001 Å °-0.085 Å °-0.2391 Å °-0.1804 Å °-0.1352 Å °0.3579 Å °0.1745 Å °
Refinement TLS groupSelection details: all

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