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- PDB-3aar: Crystal structure of Lp1NTPDase from Legionella pneumophila in co... -

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Basic information

Entry
Database: PDB / ID: 3aar
TitleCrystal structure of Lp1NTPDase from Legionella pneumophila in complex with AMPPNP
ComponentsEctonucleoside triphosphate diphosphohydrolase I
KeywordsHYDROLASE / adenosine triphosphatase / NTPDase
Function / homology
Function and homology information


nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / nucleotide binding / metal ion binding / membrane
Similarity search - Function
Exopolyphosphatase. Domain 2 / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ectonucleoside triphosphate diphosphohydrolase I
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGe, H. / Vivian, J.P. / Beddoe, T. / Rossjohn, J.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of a Legionella pneumophila Ecto -Triphosphate Diphosphohydrolase, A Structural and Functional Homolog of the Eukaryotic NTPDases
Authors: Vivian, J.P. / Riedmaier, P. / Ge, H. / Le Nours, J. / Sansom, F.M. / Wilce, M.C.J. / Byres, E. / Dias, M. / Schmidberger, J.W. / Cowan, P.J. / d'Apice, A.J.F. / Hartland, E.L. / Rossjohn, J. / Beddoe, T.
History
DepositionNov 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ectonucleoside triphosphate diphosphohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5392
Polymers40,0331
Non-polymers5061
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.701, 104.701, 75.415
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Ectonucleoside triphosphate diphosphohydrolase I


Mass: 40032.625 Da / Num. of mol.: 1 / Fragment: UNP residues 41-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: lpg1905 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q5ZUA2
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE ...ACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE REPORTED TO UNIPROT.

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.65→35 Å / Num. obs: 55849 / % possible obs: 97.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.3
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AAP

3aap


Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.63 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19717 2838 5.1 %RANDOM
Rwork0.17645 ---
obs0.17753 52982 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 31 494 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223089
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9574268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0975406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.83526155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36515502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.056155
X-RAY DIFFRACTIONr_chiral_restr0.340.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022434
X-RAY DIFFRACTIONr_nbd_refined0.2110.21590
X-RAY DIFFRACTIONr_nbtor_refined0.310.22144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2379
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.234
X-RAY DIFFRACTIONr_mcbond_it1.4451.51904
X-RAY DIFFRACTIONr_mcangle_it1.75823038
X-RAY DIFFRACTIONr_scbond_it2.88631375
X-RAY DIFFRACTIONr_scangle_it3.8654.51204
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 210 -
Rwork0.255 3925 -
obs--98.57 %

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