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- PDB-1ktg: Crystal Structure of a C. elegans Ap4A Hydrolase Binary Complex -

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Basic information

Entry
Database: PDB / ID: 1ktg
TitleCrystal Structure of a C. elegans Ap4A Hydrolase Binary Complex
ComponentsDiadenosine Tetraphosphate Hydrolase
KeywordsHYDROLASE / Nudix / AMP / Magnesium cluster
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
ADENOSINE MONOPHOSPHATE / HYDROXIDE ION / PHOSPHATE ION / Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: To be Published
Title: Crystallization of a Complex of Caenorhabditis elegans Diadenosine Tertaphosphate Hydrolase and a Non-Hydrolysable Substrate-Analogue, AppCH2ppA
Authors: Bailey, S. / Sedelnikova, S.E. / Blackburn, G.M. / Abdelghany, A.G. / McLennan, A.G. / Rafferty, J.B.
History
DepositionJan 16, 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 1.3Aug 16, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Diadenosine Tetraphosphate Hydrolase
B: Diadenosine Tetraphosphate Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,61616
Polymers31,8262
Non-polymers79014
Water5,477304
1
A: Diadenosine Tetraphosphate Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4949
Polymers15,9131
Non-polymers5818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenosine Tetraphosphate Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1227
Polymers15,9131
Non-polymers2096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.563, 36.758, 68.941
Angle α, β, γ (deg.)90.00, 114.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Diadenosine Tetraphosphate Hydrolase


Mass: 15913.135 Da / Num. of mol.: 2
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)

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Non-polymers , 5 types, 318 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, Magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
132 %(w/v)PEG40001reservoir
20.2 Mammonium acetate1reservoir
3100 mMsodium citrate1reservoirpH5.6

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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: Aug 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 62050 / Num. obs: 24019 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.84 Å / % possible all: 96.4
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 62050 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KT9

1kt9


Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.983 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22289 1217 5.1 %RANDOM
Rwork0.18796 ---
obs0.18977 22793 --
all-24010 --
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: 7.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.06 Å2
2--0.3 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 44 304 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212191
X-RAY DIFFRACTIONr_bond_other_d0.0010.021882
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9452990
X-RAY DIFFRACTIONr_angle_other_deg0.65634379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3013266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39615357
X-RAY DIFFRACTIONr_chiral_restr0.0720.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022430
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02423
X-RAY DIFFRACTIONr_nbd_refined0.2230.3460
X-RAY DIFFRACTIONr_nbd_other0.1970.31761
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.5244
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.523
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4111.51343
X-RAY DIFFRACTIONr_mcangle_it0.71522130
X-RAY DIFFRACTIONr_scbond_it1.2483848
X-RAY DIFFRACTIONr_scangle_it1.8834.5860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 79
Rwork0.194 1647
Refinement TLS params.

T33: 0.0016 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
11.9645-0.32410.16551.233-0.51260.9829-0.02430.00190.00960.0730.0176-0.0533-0.01230.0350.00670.0240.0011-0.00080.0181-0.000820.76310.267115.2202
21.6669-0.18340.08111.42760.15130.7328-0.0157-0.0885-0.01640.106-0.00220.0890.0315-0.05880.01780.0179-0.00490.00470.0161-0.003650.06767.150113.8821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1382 - 138
2X-RAY DIFFRACTION2BB4 - 1364 - 136
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 18 Å / Rfactor obs: 0.189 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.194 / Rfactor obs: 0.194

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