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- PDB-5c7t: Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Di... -

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Basic information

Entry
Database: PDB / ID: 5c7t
TitleCrystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase in complex with ADP-ribose
ComponentsNudF protein
KeywordsHYDROLASE / Nudix
Function / homology
Function and homology information


ADP-ribose diphosphatase / ADP-ribose diphosphatase activity
Similarity search - Function
NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.06 Å
AuthorsGabelli, S.B. / de la Pena, A.H. / Suarez, A. / Amzel, L.M.
CitationJournal: Plos One / Year: 2015
Title: Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
Authors: de la Pena, A.H. / Suarez, A. / Duong-Ly, K.C. / Schoeffield, A.J. / Pizarro-Dupuy, M.A. / Zarr, M. / Pineiro, S.A. / Amzel, L.M. / Gabelli, S.B.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NudF protein
B: NudF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,29720
Polymers42,5812
Non-polymers2,71618
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-144 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.594, 103.402, 51.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NudF protein


Mass: 21290.469 Da / Num. of mol.: 2 / Mutation: E140Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: nudF, Bd3179 / Plasmid: pET24
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6MIH8, ADP-ribose diphosphatase

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Non-polymers , 7 types, 230 molecules

#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.75-2.0 M ammonium sulfate, 0.1 M HEPES pH 7.0, and 0-0.5% PEG 8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.541 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 24431 / % possible obs: 95 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.095 / Χ2: 1.874 / Net I/av σ(I): 17.608 / Net I/σ(I): 11.9 / Num. measured all: 130858
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.06-2.132.10.52517262.23668.9
2.13-2.222.70.44221762.12986.3
2.22-2.323.50.37324442.1196.8
2.32-2.4450.35625142.30799.1
2.44-2.660.29125192.15698.8
2.6-2.86.10.21625452.2499.5
2.8-3.086.30.14625481.93499.8
3.08-3.526.60.08425961.566100
3.52-4.446.90.05726221.567100
4.44-506.70.05827411.40899.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
REFMAC5.8.0049refinement
REFMAC5.8.0049phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5c7Q

5c7q


Resolution: 2.06→26.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2342 / WRfactor Rwork: 0.1673 / FOM work R set: 0.8043 / SU B: 5.494 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2291 / SU Rfree: 0.1999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1256 5.2 %RANDOM
Rwork0.1812 ---
obs0.1845 23061 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.43 Å2 / Biso mean: 31.191 Å2 / Biso min: 14.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å2-0 Å20 Å2
2---0.58 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 2.06→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 169 212 3356
Biso mean--61.29 37.1 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193212
X-RAY DIFFRACTIONr_bond_other_d0.0010.023074
X-RAY DIFFRACTIONr_angle_refined_deg1.8862.0094337
X-RAY DIFFRACTIONr_angle_other_deg0.83237082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76824.156154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34115564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4971520
X-RAY DIFFRACTIONr_chiral_restr0.1070.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
X-RAY DIFFRACTIONr_mcbond_it2.2042.6921447
X-RAY DIFFRACTIONr_mcbond_other2.2022.6911446
X-RAY DIFFRACTIONr_mcangle_it3.184.0191807
LS refinement shellResolution: 2.064→2.117 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 67 -
Rwork0.274 1224 -
all-1291 -
obs--70.59 %

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