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- PDB-2o1c: Structure of the E. coli dihydroneopterin triphosphate pyrophosph... -

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Basic information

Entry
Database: PDB / ID: 2o1c
TitleStructure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase
ComponentsdATP pyrophosphohydrolase
KeywordsHYDROLASE / Nudix NTP hydrolase NTP pyrophosphohydrolase MutT dihydroneopterin triphosphate pyrophosphohydrolase folate biosynthesis
Function / homology
Function and homology information


dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / dATP diphosphatase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / magnesium ion binding / metal ion binding
Similarity search - Function
Dihydroneopterin triphosphate diphosphatase / 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
PYROPHOSPHATE / Dihydroneopterin triphosphate diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsGabelli, S.B. / Bianchet, M.A. / Amzel, L.M.
Citation
Journal: Structure / Year: 2007
Title: Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis.
Authors: Gabelli, S.B. / Bianchet, M.A. / Xu, W. / Dunn, C.A. / Niu, Z.D. / Amzel, L.M. / Bessman, M.J.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Escherichia coli orf17 codes for a nucleoside triphosphate pyrophosphohydrolase member of the MutT family of proteins. Cloning, purification, and characterization of the enzyme.
Authors: O'Handley, S.F. / Frick, D.N. / Bullions, L.C. / Mildvan, A.S. / Bessman, M.J.
#2: Journal: J.Biol.Chem. / Year: 1974
Title: The biosynthesis of folic acid. XII. Purification and properties of dihydroneopterin triphosphate pyrophosphohydrolase.
Authors: Suzuki, Y. / Brown, G.M.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: dATP pyrophosphohydrolase
B: dATP pyrophosphohydrolase
C: dATP pyrophosphohydrolase
D: dATP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,22911
Polymers69,3114
Non-polymers9187
Water11,007611
1
A: dATP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6984
Polymers17,3281
Non-polymers3703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dATP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6984
Polymers17,3281
Non-polymers3703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: dATP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5062
Polymers17,3281
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: dATP pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)17,3281
Polymers17,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.104, 42.579, 106.467
Angle α, β, γ (deg.)90.00, 115.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-191-

HOH

21B-310-

HOH

DetailsThe biological assembly is a monomer.

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Components

#1: Protein
dATP pyrophosphohydrolase


Mass: 17327.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Gene: nudB, ntpA / Plasmid: pet11b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0AFC0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 1.84 Å3/Da / Density % sol: 32.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.3-1.5 Ammonium sulfate, 1% propanol, 3-5 mM DTT, 4mM sodium pyrophosphate, 100mM Na Hepes pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22981
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X4A11.1
ROTATING ANODERIGAKU RU20021.541
Detector
TypeIDDetectorDate
FUJI1IMAGE PLATEApr 10, 1997
RIGAKU RAXIS IIC2IMAGE PLATEAug 8, 1998
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.5411
ReflectionResolution: 1.8→95.945 Å / Num. obs: 44935 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.086 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.88 Å / Rsym value: 0.342 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→95.78 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.885 / SU B: 7.09 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2238 5 %RANDOM
Rwork0.226 ---
obs0.229 44933 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.64 Å2
2---0.32 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→95.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 47 611 5364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224854
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9436611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78323.457243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03615821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.881544
X-RAY DIFFRACTIONr_chiral_restr0.0790.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023668
X-RAY DIFFRACTIONr_nbd_refined0.2060.22408
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2556
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4140.2209
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.278
X-RAY DIFFRACTIONr_mcbond_it0.5191.52999
X-RAY DIFFRACTIONr_mcangle_it0.83824715
X-RAY DIFFRACTIONr_scbond_it1.41132145
X-RAY DIFFRACTIONr_scangle_it2.1324.51896
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 181 -
Rwork0.256 3128 -
obs-3309 94.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.241-0.23380.23411.15990.17840.8666-0.0425-0.06940.05430.1719-0.0028-0.0468-0.02660.02690.0452-0.0547-0.006-0.004-0.03950.0035-0.0086-16.3532.46463.441
21.43380.0370.42770.9079-0.06080.5605-0.01250.0458-0.0329-0.1499-0.00760.03520.01170.04290.0201-0.05610.002-0.0099-0.0416-0.00820.004921.7172.53757.145
32.2248-0.11830.55871.0498-0.00131.9704-0.0583-0.2229-0.17260.1539-0.01360.0459-0.20410.07480.072-0.0017-0.0190.0127-0.01550.0388-0.1228-27.02524.30688.516
41.4696-0.27850.25411.3923-0.11340.7792-0.00690.0485-0.0403-0.029-0.06580.01240.0287-0.03340.0727-0.0318-0.00670.04310.00260.0108-0.1129.52723.66879.48
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 148
2X-RAY DIFFRACTION2B4 - 149
3X-RAY DIFFRACTION3C6 - 147
4X-RAY DIFFRACTION4D7 - 147

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