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- PDB-2pyu: Structure of the E. coli inosine triphosphate pyrophosphatase Rgd... -

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Basic information

Entry
Database: PDB / ID: 2pyu
TitleStructure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP
ComponentsInosine Triphosphate Pyrophosphatase RdgB
KeywordsHYDROLASE / ITP pyrophosphatase x-ray structure enzyme mechanism product
Function / homology
Function and homology information


XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding ...XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSinger, A.U. / Proudfoot, M. / Skarina, T. / Savchenko, A. / Yakunin, A.F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.
Authors: Savchenko, A. / Proudfoot, M. / Skarina, T. / Singer, A. / Litvinova, O. / Sanishvili, R. / Brown, G. / Chirgadze, N. / Yakunin, A.F.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine Triphosphate Pyrophosphatase RdgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7463
Polymers23,3351
Non-polymers4102
Water2,648147
1
A: Inosine Triphosphate Pyrophosphatase RdgB
hetero molecules

A: Inosine Triphosphate Pyrophosphatase RdgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4916
Polymers46,6712
Non-polymers8214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)77.941, 77.941, 81.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Inosine Triphosphate Pyrophosphatase RdgB


Mass: 23335.295 Da / Num. of mol.: 1 / Mutation: D69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yggV / Plasmid: pET15-b-based,p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RP
References: UniProt: P52061, nucleoside-triphosphate diphosphatase
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 200 mM Mg Acetate, cryoprotected with 7% each of glycerol, sucrose and ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2006 / Details: Osmic Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 31924 / Num. obs: 31488 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 37.5
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 5.5 / Num. unique all: 3168 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1K7K

1k7k


Resolution: 2.02→32.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.241 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25346 860 5.1 %RANDOM
Rwork0.19224 ---
all0.19506 ---
obs0.19506 16119 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.02→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 27 147 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.9862212
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93523.73167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6441511
X-RAY DIFFRACTIONr_chiral_restr0.1630.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021224
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2752
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21113
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5171.51067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29821653
X-RAY DIFFRACTIONr_scbond_it3.8143634
X-RAY DIFFRACTIONr_scangle_it5.6294.5559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.018→2.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 65 -
Rwork0.247 1160 -
obs-1160 99.51 %

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