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- PDB-4br9: Legionella pneumophila NTPDase1 crystal form II, closed, apo -

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Basic information

Entry
Database: PDB / ID: 4br9
TitleLegionella pneumophila NTPDase1 crystal form II, closed, apo
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
KeywordsHYDROLASE / APYRASE / ATPASE / ADPASE / CD39 / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / 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
Ectonucleoside triphosphate diphosphohydrolase I
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZebisch, M. / Schaefer, P. / Lauble, P. / Straeter, N.
CitationJournal: Structure / Year: 2013
Title: Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases
Authors: Zebisch, M. / Krauss, M. / Schaefer, P. / Lauble, P. / Straeter, N.
History
DepositionJun 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Other
Revision 1.3Dec 25, 2013Group: Structure summary
Revision 1.4Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2387
Polymers83,7612
Non-polymers4765
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-131 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.504, 86.198, 72.215
Angle α, β, γ (deg.)90.00, 107.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.426, 0.089, -0.9), (0.074, -0.995, -0.063), (-0.902, -0.039, -0.431)
Vector: 57.252, 2.987, 91.534)

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Components

#1: Protein ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I / NTPDASE1


Mass: 41880.594 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZUA2, apyrase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 44.5 % / Description: NONE
Crystal growpH: 5.5 / Details: 9% PEG3350, 100MM (NH4)2SO4, 100MM NAMES PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.2144
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2144 Å / Relative weight: 1
ReflectionResolution: 1.4→29 Å / Num. obs: 138132 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.2 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.69 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17113 2070 1.5 %RANDOM
Rwork0.12736 ---
obs0.12798 136028 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20.25 Å2
2--0.13 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 26 648 6445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9438744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.25926.269327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.509151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.745159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215007
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.39936340
X-RAY DIFFRACTIONr_sphericity_free32.5995163
X-RAY DIFFRACTIONr_sphericity_bonded19.28556613
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 106 -
Rwork0.205 7073 -
obs--67.74 %

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