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- PDB-3q1p: Crystal structure of CDP-Chase -

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Basic information

Entry
Database: PDB / ID: 3q1p
TitleCrystal structure of CDP-Chase
ComponentsPhosphohydrolase (MutT/nudix family protein)
KeywordsHYDROLASE / Nudix / asymmetric dimer / RNA exonuclease / CDP-choline pyrophosphatase
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1120 / Hydrolase of X-linked nucleoside diphosphate N terminal / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1120 / Hydrolase of X-linked nucleoside diphosphate N terminal / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phosphohydrolase (MutT/nudix family protein)
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDuong-Ly, K.C. / Gabelli, S.B. / Amzel, L.M.
CitationJournal: J.Bacteriol. / Year: 2011
Title: The Nudix Hydrolase CDP-Chase, a CDP-Choline Pyrophosphatase, Is an Asymmetric Dimer with Two Distinct Enzymatic Activities.
Authors: Duong-Ly, K.C. / Gabelli, S.B. / Xu, W. / Dunn, C.A. / Schoeffield, A.J. / Bessman, M.J. / Amzel, L.M.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphohydrolase (MutT/nudix family protein)
B: Phosphohydrolase (MutT/nudix family protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0994
Polymers47,9072
Non-polymers1922
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-79 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.471, 71.426, 111.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphohydrolase (MutT/nudix family protein)


Mass: 23953.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC2032, BC_2032 / Plasmid: pET-24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81EE8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.2 to 0.3 M Lithium sulfate, 26 to 29% PEG-4000, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97989 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 45135 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.078 / Χ2: 1.478 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8612.40.56144340.502199.5
1.86-1.94140.3944420.5371100
1.94-2.0314.20.2544520.5951100
2.03-2.1314.30.18144700.6351100
2.13-2.2714.40.13944630.7241100
2.27-2.4414.50.11444840.8991100
2.44-2.6914.70.09545061.211100
2.69-3.0814.80.07645321.6311100
3.08-3.8814.80.05845832.4681100
3.88-50140.05847695.173199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.1867 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8438 / SU B: 2.658 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1291 / SU Rfree: 0.1282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 2272 5 %RANDOM
Rwork0.1943 ---
obs0.1965 45059 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.35 Å2 / Biso mean: 26.2041 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 10 395 3655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223360
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9484541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4225399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12625.583163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.049158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022518
X-RAY DIFFRACTIONr_nbd_refined0.1940.21589
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.217
X-RAY DIFFRACTIONr_mcbond_it1.1491.52071
X-RAY DIFFRACTIONr_mcangle_it1.27423240
X-RAY DIFFRACTIONr_scbond_it2.23731501
X-RAY DIFFRACTIONr_scangle_it3.3594.51301
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 162 -
Rwork0.273 3043 -
all-3205 -
obs--97.83 %

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