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- PDB-2w4e: Structure of an N-terminally truncated Nudix hydrolase DR2204 fro... -

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Basic information

Entry
Database: PDB / ID: 2w4e
TitleStructure of an N-terminally truncated Nudix hydrolase DR2204 from Deinococcus radiodurans
ComponentsMUTT/NUDIX FAMILY PROTEIN
KeywordsHYDROLASE / ADP-RIBOSE PYROPHOSPHATASE
Function / homology
Function and homology information


nucleoside phosphate metabolic process / ribose phosphate metabolic process / hydrolase activity / cytosol
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MutT/nudix family protein
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGoncalves, A.M.D. / Fioravanti, E. / Stelter, M. / McSweeney, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of an N-Terminally Truncated Nudix Hydrolase Dr2204 from Deinococcus Radiodurans.
Authors: Goncalves, A.M.D. / Fioravanti, E. / Stelter, M. / Mcsweeney, S.
History
DepositionNov 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MUTT/NUDIX FAMILY PROTEIN
B: MUTT/NUDIX FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,2142
Polymers31,2142
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-16.13 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.301, 61.301, 165.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MUTT/NUDIX FAMILY PROTEIN / ADP-RIBOSE PYROPHOSPHATASE


Mass: 15606.864 Da / Num. of mol.: 2 / Fragment: RESIDUES 56-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PET151-D/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RSC1, ADP-ribose diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.59 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7 / Details: 0.2 M LINO3 20% W/V POLYETHYLENE GLYCOL 3350, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 18, 2008 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22215 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
REFMAC5.5.0038refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→57.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.907 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE SIDE CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY AT 1 SIGMA WERE REMOVED FROM THE MODEL. THE FINAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE SIDE CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY AT 1 SIGMA WERE REMOVED FROM THE MODEL. THE FINAL MODEL CONSISTS OF AN N-TERMINALLY TRUNCATED FORM OF THE PROTEIN MISSING THE FIRST 55 RESIDUES IN THE SEQUENCE OF MONOMER A AND FIRST 59 RESIDUES IN MONOMER B. IN BOTH MONOMERS THE ELECTRON DENSITY IS POOR FOR A SHORT LOOP RESPECTIVELY. NO MODEL COULD BE BUILT IN THIS REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1134 5.1 %RANDOM
Rwork0.208 ---
obs0.21 21034 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 2→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 0 144 2171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5832.0022830
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95722.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59215326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6731520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9671.51332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65222136
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43744
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9714.5694
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 88
Rwork0.238 1531

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