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- PDB-2b0v: NUDIX hydrolase from Nitrosomonas europaea. -

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Basic information

Entry
Database: PDB / ID: 2b0v
TitleNUDIX hydrolase from Nitrosomonas europaea.
ComponentsNUDIX hydrolase
KeywordsUNKNOWN FUNCTION / structural genomics / NUDIX hydrolase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


thiamine diphosphate phosphatase activity / nucleoside diphosphate phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribonucleoside triphosphate phosphatase activity
Similarity search - Function
Phosphatase NudJ / 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
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsOsipiuk, J. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray structure of NUDIX hydrolase from Nitrosomonas europaea.
Authors: Osipiuk, J. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUDIX hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5654
Polymers17,4441
Non-polymers1213
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NUDIX hydrolase
hetero molecules

A: NUDIX hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1308
Polymers34,8882
Non-polymers2416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2750 Å2
ΔGint-50 kcal/mol
Surface area14800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.450, 66.509, 73.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

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Components

#1: Protein NUDIX hydrolase


Mass: 17444.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: NE0184 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82XR9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.2 M NaCl, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 20171 / Num. obs: 16520 / % possible obs: 81.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 33.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.59 / Num. unique all: 281 / % possible all: 22.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 2.225 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET. THE FOLLOWING SOFTWARE WAS ALSO USED FOR PHASING: SHELXD, MLPHARE, DM, SOLVE/RESOLVE, HKL-3000
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 1681 -RANDOM
Rwork0.1669 ---
all0.1677 16498 --
obs0.1677 16498 81.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2--1.76 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 6 164 1345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221260
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9671724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79123.62158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04715218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.465159
X-RAY DIFFRACTIONr_chiral_restr0.1190.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02966
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2562
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2864
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0860.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0281.5765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82221252
X-RAY DIFFRACTIONr_scbond_it2.6663512
X-RAY DIFFRACTIONr_scangle_it4.1844.5463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 39 -
Rwork0.222 357 -
obs-357 24.67 %
Refinement TLS params.Method: refined / Origin x: 17.8767 Å / Origin y: 14.4585 Å / Origin z: 7.2567 Å
111213212223313233
T-0.028 Å20.0045 Å2-0.0009 Å2--0.0204 Å20.0044 Å2---0.027 Å2
L1.2649 °20.2952 °20.6432 °2-0.2321 °20.2419 °2--1.0291 °2
S-0.0329 Å °0.044 Å °0.0298 Å °-0.0022 Å °-0.0106 Å °0.018 Å °0.0102 Å °0.0001 Å °0.0435 Å °

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