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- PDB-4br0: rat NTPDase2 in complex with Ca AMPNP -

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Basic information

Entry
Database: PDB / ID: 4br0
Titlerat NTPDase2 in complex with Ca AMPNP
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
KeywordsHYDROLASE / APYRASE / ATPASE / ADPASE / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / NTPDASE
Function / homology
Function and homology information


purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / nucleoside diphosphate 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 / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane / cellular response to interleukin-6 / basement membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribonucleoside triphosphate phosphatase activity / platelet activation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / cell body / G protein-coupled receptor signaling pathway / cell surface / ATP hydrolysis activity / ATP binding / 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
Chem-AU1 / 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
Revision 1.3Oct 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6268
Polymers50,6991
Non-polymers9277
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.170, 69.130, 164.510
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 / NTPDASE 2 / CD39 ANTIGEN-LIKE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 2 / ECTO-ATPDASE 2 / ECTO-ATPASE 2 / NTPDASE2


Mass: 50699.027 Da / Num. of mol.: 1 / Fragment: 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: O35795, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, apyrase
#2: Chemical ChemComp-AU1 / 5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine / Adenosine 5-(alpha,beta-imido)diphosphate


Mass: 426.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details(3S)-3-HYDROXY-1-METHYL-2,3-DIHYDRO-1H-INDOLE-5,6-DIONE (AU1): AMPNP ADP ANALOG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 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→36.7 Å / Num. obs: 30057 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16

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Processing

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

Resolution: 2.05→19.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.92 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21847 1071 3.6 %RANDOM
Rwork0.16904 ---
obs0.17077 28937 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.044 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2---0.43 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 58 189 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9624651
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55423.046151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51415529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0261524
X-RAY DIFFRACTIONr_chiral_restr0.1330.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212594
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
Rfree0.33 70 -
Rwork0.232 2074 -
obs--99.31 %
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)
11.1301-0.176-0.64231.69590.9421.83380.12560.1250.2043-0.3821-0.007-0.0472-0.570.0037-0.11850.1923-0.00010.02780.06710.01420.074620.251840.38169.6928
20.9028-0.0897-0.51081.5550.48951.56860.0220.14610.0621-0.24220.0339-0.054-0.11320.1615-0.0560.0442-0.00790.02340.1453-0.02740.078525.094926.48059.7885
32.324-2.1478-3.8635.40384.65936.7744-0.13470.1914-0.07960.1027-0.02070.22770.2014-0.28120.15540.0511-0.01220.01310.221-0.05550.130126.082511.0428-3.9238
40.6427-0.14520.05511.11010.66871.7604-0.0685-0.06-0.0420.14230.0672-0.08120.20780.12870.00130.03630.0312-0.00090.1224-0.00260.084124.529622.427730.1007
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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