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- PDB-5c8l: Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Di... -

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Basic information

Entry
Database: PDB / ID: 5c8l
TitleCrystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase
ComponentsNudF protein
KeywordsHYDROLASE / Nudix
Function / homology
Function and homology information


ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / cytosol
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
alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,99215
Polymers42,5812
Non-polymers1,41113
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-120 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.947, 103.279, 51.744
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 / Sugars , 2 types, 4 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
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 331 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
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: 1.8→50 Å / Num. obs: 35689 / % possible obs: 92.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.064 / Χ2: 2.694 / Net I/av σ(I): 42.841 / Net I/σ(I): 19.1 / Num. measured all: 201670
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.863.40.46620651.59754.4
1.86-1.943.80.35428821.8875.8
1.94-2.034.80.25235832.13794.4
2.03-2.135.90.1937992.43199.4
2.13-2.275.90.15538162.73899.5
2.27-2.4460.12838062.78499.7
2.44-2.696.20.09638452.8499.9
2.69-3.086.40.0738822.94399.9
3.08-3.886.20.04939163.00499.9
3.88-506.30.04340953.04499.6

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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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2048 / WRfactor Rwork: 0.16 / FOM work R set: 0.8594 / SU B: 2.697 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1291 / SU Rfree: 0.1249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1805 5.1 %RANDOM
Rwork0.1667 ---
obs0.1689 33842 92.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 28.662 Å2 / Biso min: 15.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å20 Å2
2---1.3 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 85 320 3380
Biso mean--52.1 36.99 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193164
X-RAY DIFFRACTIONr_bond_other_d0.0020.023038
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9814280
X-RAY DIFFRACTIONr_angle_other_deg0.78636993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15124.167156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_mcbond_it1.8242.5061464
X-RAY DIFFRACTIONr_mcbond_other1.8142.5051463
X-RAY DIFFRACTIONr_mcangle_it2.6853.7431834
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 77 -
Rwork0.298 1375 -
all-1452 -
obs--51.18 %

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