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- PDB-4hfq: Crystal structure of UDP-X diphosphatase -

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Basic information

Entry
Database: PDB / ID: 4hfq
TitleCrystal structure of UDP-X diphosphatase
ComponentsMutT/nudix family protein
KeywordsHYDROLASE / UDP-sugar diphosphatase / Nudix / RNA exonuclease / pyrophosphatase / Mur pathway
Function / homology
Function and homology information


Hydrolase of X-linked nucleoside diphosphate N terminal / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / MutT/nudix family protein / MutT/nudix family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsDuong-Ly, K.C. / Amzel, L.M. / Gabelli, S.B.
CitationJournal: Plos One / Year: 2013
Title: A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis.
Authors: Duong-Ly, K.C. / Woo, H.N. / Dunn, C.A. / Xu, W. / Babic, A. / Bessman, M.J. / Amzel, L.M. / Gabelli, S.B.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,64432
Polymers46,9872
Non-polymers2,65730
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-50 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.992, 77.992, 64.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Details/

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MutT/nudix family protein


Mass: 23493.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP1669, SP_1669 / Plasmid: pET-24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97PF7, UniProt: A0A0H2URA0*PLUS

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Non-polymers , 7 types, 539 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis-Tris, Li2SO4, PEG-3350, pH 5.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 12, 2008
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Av σ(I) over netI: 27.56 / Number: 182809 / Rmerge(I) obs: 0.122 / Χ2: 1.07 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 31951 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25010010.0712.2165.8
3.334.210010.0681.3535.8
2.913.3310010.0951.0215.8
2.652.9110010.1360.9635.8
2.462.6510010.1840.9345.8
2.312.4610010.2240.8655.8
2.22.3110010.2950.9435.8
2.12.210010.3380.8035.7
2.022.110010.4150.8125.6
1.952.0210010.5540.7685.2
ReflectionResolution: 1.39→67.57 Å / Num. obs: 88640 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.057 / Χ2: 0.696 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.39-1.443.90.49688810.9551100
1.44-1.54.20.29288530.5641100
1.5-1.574.70.22888480.5271100
1.57-1.655.40.288760.5341100
1.65-1.755.70.16188680.5911100
1.75-1.895.80.11688410.6091100
1.89-2.085.80.07988660.6451100
2.08-2.385.80.05788980.71100
2.38-2.995.90.04788430.8071100
2.99-505.80.03588661.039199.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.39→67.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.911 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 4437 5 %RANDOM
Rwork0.1724 ---
obs0.1736 84088 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.82 Å2 / Biso mean: 16.2237 Å2 / Biso min: 6.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.39→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 167 509 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023756
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9925063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4925460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28725.368190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30215671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7091521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212837
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 306 -
Rwork0.266 6230 -
all-6536 -
obs--99.48 %

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