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- PDB-6mjk: Crystal Structure of dUTP pyrophosphatase protein, from Naegleria... -

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Basic information

Entry
Database: PDB / ID: 6mjk
TitleCrystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine
ComponentsdUTP pyrophosphatase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dUTP pyrophosphatase protein
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE / PYROPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine
Authors: Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2985
Polymers16,8431
Non-polymers4554
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.230, 74.230, 74.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-202-

MG

21A-359-

HOH

31A-413-

HOH

41A-431-

HOH

51A-439-

HOH

61A-461-

HOH

71A-463-

HOH

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Components

#1: Protein dUTP pyrophosphatase / NafoA.01242.a.B1


Mass: 16843.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z0YU86
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUR / 2'-DEOXYURIDINE / Deoxyuridine


Mass: 228.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O5 / Comment: antivirus*YM
#4: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+ C6: 40% PEG 300 + 100mM Sodium phosphate dibasic / sodium citrate pH 4.2:cryo:direct. PW37974 22.5mg/mL, 0.4+0.4, 6 mM dUTP + 6 mM MgCl2 puck xbp1-8, tray286723C6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→33.197 Å / Num. obs: 24498 / % possible obs: 100 % / Redundancy: 16.992 % / Biso Wilson estimate: 21.781 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.041 / Χ2: 1.034 / Net I/σ(I): 46.35 / Num. measured all: 416266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.4916.9770.4975.7918010.9590.512100
1.49-1.5316.8740.4157.2217370.9740.427100
1.53-1.5717.0050.3259.216980.9830.335100
1.57-1.6217.0710.251216680.9880.258100
1.62-1.6717.1590.19515.615860.9940.201100
1.67-1.7317.1480.15719.4815430.9960.162100
1.73-1.817.2220.12524.5115010.9970.129100
1.8-1.8717.2040.09432.5114440.9990.096100
1.87-1.9617.1070.07539.813970.9990.077100
1.96-2.0517.2280.05850.4413020.9990.06100
2.05-2.1617.2140.04859.89126510.049100
2.16-2.2917.0170.04169.57120710.042100
2.29-2.4517.10.03676.56111910.037100
2.45-2.6516.8590.03383.9105910.034100
2.65-2.917.10.02796.8897110.028100
2.9-3.2417.0470.022109.3988710.023100
3.24-3.7416.8950.019124.4178910.019100
3.74-4.5916.7360.016130.7567010.017100
4.59-6.4816.1140.017128.9453310.018100
6.48-33.19713.0030.0211632110.02199.1

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Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOP

4oop


Resolution: 1.45→33.197 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 2039 8.33 %
Rwork0.1339 --
obs0.1369 24472 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→33.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 27 166 1275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051203
X-RAY DIFFRACTIONf_angle_d0.7831652
X-RAY DIFFRACTIONf_dihedral_angle_d14.627461
X-RAY DIFFRACTIONf_chiral_restr0.081186
X-RAY DIFFRACTIONf_plane_restr0.004233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4499-1.48370.18271290.12961510X-RAY DIFFRACTION100
1.4837-1.52080.16911230.12521476X-RAY DIFFRACTION100
1.5208-1.56190.20191510.1191469X-RAY DIFFRACTION100
1.5619-1.60780.17221460.121455X-RAY DIFFRACTION100
1.6078-1.65970.18751500.11741467X-RAY DIFFRACTION100
1.6597-1.7190.18271290.11541496X-RAY DIFFRACTION100
1.719-1.78790.17471300.11961471X-RAY DIFFRACTION100
1.7879-1.86920.15191020.12371515X-RAY DIFFRACTION100
1.8692-1.96780.1691270.12421494X-RAY DIFFRACTION100
1.9678-2.0910.15761430.1261485X-RAY DIFFRACTION100
2.091-2.25250.16651400.1281489X-RAY DIFFRACTION100
2.2525-2.47910.17881530.13651500X-RAY DIFFRACTION100
2.4791-2.83760.16021460.1491493X-RAY DIFFRACTION100
2.8376-3.57440.16971390.14291518X-RAY DIFFRACTION100
3.5744-33.20540.16831310.14111595X-RAY DIFFRACTION100

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