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- PDB-3s86: Crystal Structure of TM0159 with bound IMP -

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Basic information

Entry
Database: PDB / ID: 3s86
TitleCrystal Structure of TM0159 with bound IMP
ComponentsNucleoside-triphosphatase
KeywordsHYDROLASE / long twisted beta strand covered by two lobes / non-canonical nucleoside triphosphatase
Function / homology
Function and homology information


purine nucleoside triphosphate catabolic process / XTP/dITP diphosphatase / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / ribonucleoside triphosphate phosphatase activity / cytosol
Similarity search - Function
dITP/XTP pyrophosphatase / Maf protein - #10 / Ham1-like protein / Ham1 family / Maf protein / Inosine triphosphate pyrophosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSommerhalter, M. / Smith, C. / Awwad, K. / Desai, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima.
Authors: Awwad, K. / Desai, A. / Smith, C. / Sommerhalter, M.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Derived calculations / Other
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside-triphosphatase
B: Nucleoside-triphosphatase
C: Nucleoside-triphosphatase
D: Nucleoside-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,11512
Polymers95,3384
Non-polymers1,7778
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-123 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.400, 75.990, 157.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside-triphosphatase / Nucleoside triphosphate phosphohydrolase / NTPase


Mass: 23834.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0159 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: Q9WY06, nucleoside-triphosphate phosphatase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG3350, L-Proline, Tris-HCl pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 48209 / Num. obs: 48090 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.15→2.2 Å / Mean I/σ(I) obs: 3.05 / Num. unique all: 3160 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.156 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 2405 5 %RANDOM
Rwork0.22 ---
obs0.2229 48086 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.39 Å2 / Biso mean: 46.8774 Å2 / Biso min: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 0 112 196 6257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0226201
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9988374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56123.625251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.109151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.081532
X-RAY DIFFRACTIONr_chiral_restr0.130.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214548
X-RAY DIFFRACTIONr_mcbond_it1.0491.53758
X-RAY DIFFRACTIONr_mcangle_it1.85826077
X-RAY DIFFRACTIONr_scbond_it3.12432443
X-RAY DIFFRACTIONr_scangle_it4.9224.52297
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 175 -
Rwork0.305 3318 -
all-3493 -
obs--100 %

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