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- PDB-4bqz: Rat NTPDase2 in complex with Mg GMPPNP -

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Basic information

Entry
Database: PDB / ID: 4bqz
TitleRat NTPDase2 in complex with Mg GMPPNP
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
KeywordsHYDROLASE / APYRASE / ATPASE / ADPASE / CD39 / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / NTPDASE
Function / homology
Function and homology information


purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / UDP phosphatase activity / GDP phosphatase activity / ADP phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane ...purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / UDP phosphatase activity / GDP phosphatase activity / ADP phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane / cellular response to interleukin-6 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / basement membrane / ribonucleoside triphosphate phosphatase activity / platelet activation / cell body / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / hydrolase activity / G protein-coupled receptor signaling pathway / cell surface / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / 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-GUANYLATE ESTER / Ectonucleoside triphosphate diphosphohydrolase 2 / Ectonucleoside triphosphate diphosphohydrolase 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.05 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 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5226
Polymers50,6991
Non-polymers8235
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.880, 69.760, 163.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2 / NTPDASE2


Mass: 50699.027 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 28-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5RJP4, UniProt: O35795*PLUS, apyrase
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.31 Å3/Da / Density % sol: 46.72 % / Description: NONE
Crystal growpH: 7.3 / Details: 100 MM HEPES/NAOH PH 7.3, 2% PEG6000, 3MM NAN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→36.6 Å / Num. obs: 30277 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.05→36.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.429 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23136 1533 5.1 %RANDOM
Rwork0.1828 ---
obs0.18527 28778 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.09 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.05→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 51 132 3454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9624670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06722.922154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49415536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6141526
X-RAY DIFFRACTIONr_chiral_restr0.1370.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212617
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 114 -
Rwork0.26 2059 -
obs--100 %
Refinement TLS params.

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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8462-0.066-0.5721.16321.11091.61080.08850.06310.2225-0.3694-0.010.036-0.5769-0.0329-0.07850.29170.01570.00070.01660.02460.067420.183940.81199.4712
22.3217-0.20511.10011.50630.51830.83630.0070.10470.064-0.17480.0184-0.10620.00620.0972-0.02540.14770.01910.02080.0394-0.01970.029925.307126.89769.7929
31.9957-1.9306-3.10785.00255.38716.6581-0.17940.0659-0.05540.03950.09130.09640.1780.00830.0880.1316-0.01660.01270.1135-0.02580.10426.375411.3231-3.8403
40.6275-0.2638-0.17161.37340.4041.2618-0.1007-0.0967-0.02460.26080.082-0.08920.17570.11060.01860.13350.0424-0.00090.0503-0.00170.015924.714522.899930.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 162
2X-RAY DIFFRACTION1A436 - 461
3X-RAY DIFFRACTION2A163 - 179
4X-RAY DIFFRACTION2A427 - 435
5X-RAY DIFFRACTION3A180 - 195
6X-RAY DIFFRACTION4A196 - 426

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