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- PDB-7d62: pGpG-specific phosphodiesterase - PggH from Vibrio cholrae -

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Basic information

Entry
Database: PDB / ID: 7d62
TitlepGpG-specific phosphodiesterase - PggH from Vibrio cholrae
ComponentsPggH
KeywordsSIGNALING PROTEIN / pGpG / phosphodiesterase / nanornase
Function / homologyUncharacterised conserved protein UCP028235 / DHH phosphoesterase superfamily / metal ion binding / : / Exopolyphosphatase-related protein
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHa, N.-C. / Jang, Y.
CitationJournal: To Be Published
Title: A pGpG-specific phosphodiesterase
Authors: Lee, J.-W. / Heo, K. / Jang, Y. / Ha, N.-C. / Seok, Y.-J.
History
DepositionSep 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: PggH
B: PggH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3206
Polymers74,0182
Non-polymers3024
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-49 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.367, 148.830, 58.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein PggH


Mass: 37008.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0593 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KLZ6
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2 M manganese chloride, Tris-HCl (pH 8.5), 12% (v/v) PEG 4000, 2 mM Tris(2-carboxyethyl) phosphine (TCEP)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 48026 / % possible obs: 99.3 % / Redundancy: 8.4 % / Biso Wilson estimate: 17.9 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.091 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2320 / CC1/2: 0.394 / Rpim(I) all: 0.251 / Rrim(I) all: 0.578 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: 000)refinement
XDSdata reduction
HKL-2000v712data scaling
PHENIX(1.11.1_2575)phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 2000 4.55 %
Rwork0.1959 --
obs0.1979 43968 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 12 74 4796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094816
X-RAY DIFFRACTIONf_angle_d0.9486516
X-RAY DIFFRACTIONf_dihedral_angle_d5.699633
X-RAY DIFFRACTIONf_chiral_restr0.057721
X-RAY DIFFRACTIONf_plane_restr0.005841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.3327710.32341494X-RAY DIFFRACTION46
1.94-20.3791970.2892034X-RAY DIFFRACTION63
2-2.060.2891180.25532492X-RAY DIFFRACTION77
2.06-2.120.27741390.20822908X-RAY DIFFRACTION89
2.12-2.20.26251520.21393163X-RAY DIFFRACTION97
2.2-2.290.2481520.2053220X-RAY DIFFRACTION99
2.29-2.390.22731550.19293253X-RAY DIFFRACTION100
2.39-2.520.25241570.20013282X-RAY DIFFRACTION100
2.52-2.670.2751570.19983287X-RAY DIFFRACTION100
2.67-2.880.25031570.21453289X-RAY DIFFRACTION100
2.88-3.170.2551570.21383317X-RAY DIFFRACTION100
3.17-3.630.2261600.19593336X-RAY DIFFRACTION100
3.63-4.570.20541610.15753373X-RAY DIFFRACTION100
4.57-38.250.19921670.16893520X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33360.49710.29082.5946-0.36642.23570.0281-0.04170.22480.21460.03660.1925-0.43310.0045-0.02680.1949-0.00110.01690.0853-0.0260.11225.69594.712617.7945
22.0262-0.77730.23373.1098-0.18982.42960.11120.03330.23160.0447-0.0573-0.4775-0.12410.39510.01640.1073-0.0377-0.04820.1532-0.00850.081134.737987.764717.8823
31.79580.41231.83230.8131.08844.16640.051-0.31670.03870.196-0.06830.0729-0.0712-0.36560.00450.1466-0.01570.0080.13770.00270.119113.133179.352411.314
40.7237-0.12280.42352.2346-1.14351.1809-0.01410.0361-0.0372-0.03540.04920.11640.0288-0.1075-0.03330.03130.0228-0.02420.1267-0.03370.082613.653580.8375-9.4872
51.18861.3121-1.09033.8983-2.74923.9516-0.00460.13110.188-0.0499-0.0656-0.588-0.00940.61990.25670.04950.0053-0.03180.25990.03170.351827.695679.5113-10.8539
62.6191-0.41460.8543.1628-0.19582.00510.00320.3150.0211-0.3532-0.1657-0.41540.0780.12550.07940.0610.01240.02710.2007-0.00170.119721.583584.1188-18.149
72.5660.5326-0.57743.49280.70124.2080.02190.44190.0167-0.6970.10550.30120.16-0.0364-0.06580.3785-0.0575-0.1090.3518-0.01610.2087-12.267694.3634-26.957
82.59151.6735-0.31074.98530.18712.1369-0.07490.0925-0.30720.23950.08250.10870.2375-0.084-0.00160.17040.02620.05110.1303-0.00940.2725-9.7897.0974-8.75
92.455-0.31530.02131.1770.23180.32560.0394-0.04130.15690.156-0.0259-0.0609-0.06270.0804-0.01860.16880.005-0.0250.0828-0.0010.091511.8291104.7505-6.3386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 259 )
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 277 )
6X-RAY DIFFRACTION6chain 'A' and (resid 278 through 310 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 118 )
8X-RAY DIFFRACTION8chain 'B' and (resid 119 through 181 )
9X-RAY DIFFRACTION9chain 'B' and (resid 182 through 310 )

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