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- PDB-1kt9: Crystal Structure of C. elegans Ap4A Hydrolase -

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Basic information

Entry
Database: PDB / ID: 1kt9
TitleCrystal Structure of C. elegans Ap4A Hydrolase
ComponentsDiadenosine Tetraphosphate Hydrolase
KeywordsHYDROLASE / Nudix
Function / homology
Function and homology information


5-phosphoribosyl 1-pyrophosphate pyrophosphatase activity / diadenosine tetraphosphate catabolic process / Detoxification of Reactive Oxygen Species / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ADP biosynthetic process / ribose phosphate metabolic process / ATP biosynthetic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / apoptotic process / ATP binding
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase / : / 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 ...Bis(5'-nucleosyl)-tetraphosphatase / : / 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
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsBailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, H.M. / Baker, P.J. / McLennan, A.G. / Rafferty, J.B.
Citation
Journal: Structure / Year: 2002
Title: The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms
Authors: Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, H.M. / Baker, P.J. / McLennan, A.G. / Rafferty, J.B.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2001
Title: Cloning, characterisation and crystallisation of a diadenosine 5',5"'-P(1),P(4)-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans.
Authors: Abdelghany, H.M. / Gasmi, L. / Cartwright, J.L. / Bailey, S. / Rafferty, J.B. / McLennan, A.G.
History
DepositionJan 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diadenosine Tetraphosphate Hydrolase


Theoretical massNumber of molelcules
Total (without water)15,9131
Polymers15,9131
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.794, 72.934, 61.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Diadenosine Tetraphosphate Hydrolase


Mass: 15913.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Y37H9A.6 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9U2M7, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMAppCH2ppA1drop
210 mM1dropMgCl2
330 %(w/v)PEG40001reservoir
40.2 M1reservoirMgCl2
5Tris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.98→18 Å / Num. all: 53439 / Num. obs: 9864 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 1.98→2.05 Å / % possible all: 97.9
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 97.9 % / Num. measured all: 53439 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 9.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.165 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.15 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 474 4.8 %RANDOM
Rwork0.19631 ---
obs0.19715 9389 98 %-
all-9389 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 0 98 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211061
X-RAY DIFFRACTIONr_bond_other_d0.0010.02927
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9291447
X-RAY DIFFRACTIONr_angle_other_deg0.81232148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2483129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8115170
X-RAY DIFFRACTIONr_chiral_restr0.0960.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02211
X-RAY DIFFRACTIONr_nbd_refined0.2470.3249
X-RAY DIFFRACTIONr_nbd_other0.2170.3813
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.573
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4320.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.511
X-RAY DIFFRACTIONr_mcbond_it0.8931.5658
X-RAY DIFFRACTIONr_mcangle_it1.52821043
X-RAY DIFFRACTIONr_scbond_it2.2483403
X-RAY DIFFRACTIONr_scangle_it3.4164.5404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 38
Rwork0.203 695
Refinement TLS params.Method: refined / Origin x: 18.7636 Å / Origin y: 14.3648 Å / Origin z: 8.2546 Å
111213212223313233
T0.0159 Å2-0.0126 Å2-0.0051 Å2-0.0115 Å2-0.0044 Å2--0.048 Å2
L3.0018 °2-0.6607 °20.1886 °2-2.4865 °2-0.2974 °2--4.0488 °2
S-0.0196 Å °-0.0561 Å °-0.2416 Å °-0.0172 Å °-0.0036 Å °0.163 Å °0.2561 Å °-0.1076 Å °0.0232 Å °
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 18 Å / Rfactor obs: 0.201 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.203

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