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- PDB-3zx2: NTPDase1 in complex with Decavanadate -

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Basic information

Entry
Database: PDB / ID: 3zx2
TitleNTPDase1 in complex with Decavanadate
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
KeywordsHYDROLASE / DOMAIN ROTATION / POLYOXOMETALLATE / METAL CLUSTER / PURINERGIC SIGNALING N
Function / homology
Function and homology information


response to proline / CDP phosphatase activity / apyrase / apyrase activity / ITPase activity / nucleoside diphosphate catabolic process / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / nucleoside diphosphate phosphatase activity ...response to proline / CDP phosphatase activity / apyrase / apyrase activity / ITPase activity / nucleoside diphosphate catabolic process / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion / ADP phosphatase activity / CTPase activity / GDP phosphatase activity / cellular response to interferon-alpha / ADP catabolic process / response to L-arginine / negative regulation of dopamine secretion / negative regulation of ATP biosynthetic process / response to auditory stimulus / response to caffeine / response to ATP / basement membrane / ribonucleoside triphosphate phosphatase activity / response to gamma radiation / synaptic membrane / caveola / platelet activation / platelet aggregation / synaptic vesicle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / basolateral plasma membrane / response to lipopolysaccharide / G protein-coupled receptor signaling pathway / external side of plasma membrane / GTPase activity / neuronal cell body / cell surface / ATP hydrolysis activity / extracellular space / 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
ACETIC ACID / DECAVANADATE / Ectonucleoside triphosphate diphosphohydrolase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.81 Å
AuthorsZebisch, M. / Schaefer, P. / Straeter, N.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystallographic Evidence for a Domain Motion in Rat Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) 1.
Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Strater, N.
History
DepositionAug 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Jan 31, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Oct 9, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / 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: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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 1
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,57544
Polymers202,3724
Non-polymers5,20340
Water12,755708
1
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,65818
Polymers101,1862
Non-polymers2,47216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,91726
Polymers101,1862
Non-polymers2,73124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.920, 80.985, 165.517
Angle α, β, γ (deg.)90.00, 117.49, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.931, 0.354, 0.088), (0.33, 0.715, 0.617), (0.155, 0.604, -0.782)33.012, -46.697, 142.05
2given(-0.995, 0.073, 0.074), (-0.103, -0.782, -0.614), (0.013, -0.619, 0.786)40.613, 47.104, 95.93
3given(0.961, -0.215, -0.176), (-0.212, -0.977, 0.039), (-0.181, -0.001, -0.984)9.55, 48.779, 98.508

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 / NTPDASE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 1 / ECTO-ATPDASE 1 / ECTO-ATPASE 1 / ECTO-APYRASE / ...NTPDASE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 1 / ECTO-ATPDASE 1 / ECTO-ATPASE 1 / ECTO-APYRASE / LYMPHOID CELL ACTIVATION ANTIGEN / CD39


Mass: 50592.953 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 38-189,206-477
Source method: isolated from a genetically manipulated source
Details: A PUTATIVE MEMBRANE INTERACTION LOOP 190TQEQSWLNFISDSQKQA206 WAS REPLACED BY A SHORTER LINKER KTPGGS
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET45B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P97687, apyrase

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Non-polymers , 5 types, 748 molecules

#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O28V10
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, ...THE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, AND 227 MATCH THE GENBANK SEQUENCE.

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 4 / Details: 3.7M NACL, 100MM NAACETAT PH 4.0

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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 / Date: Dec 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.81→39 Å / Num. obs: 127469 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 1.809→1.856 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.81→146.83 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.641 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22387 1270 1 %RANDOM
Rwork0.17547 ---
obs0.17597 126089 73.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å2-0.25 Å2
2--1.27 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 1.81→146.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12518 0 209 708 13435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.99118330
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02751618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14824.661575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.084152217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0971531
X-RAY DIFFRACTIONr_chiral_restr0.1420.21870
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219885
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: 1.809→1.856 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 7 -
Rwork0.258 380 -
obs--3.02 %
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)
12.77521.0569-1.02324.0715-2.21884.7373-0.13370.0507-0.4235-0.2578-0.0523-0.28150.93730.33260.1860.36030.1126-0.01050.2151-0.0140.16831.5343-10.653697.9506
27.73970.0944-0.02765.5582-2.97867.7355-0.01960.4593-0.6113-0.0976-0.03980.19571.0622-0.540.05940.2586-0.0876-0.02630.2292-0.03940.165115.1216-5.719497.1501
31.93040.3481.40630.75680.68363.9086-0.05360.110.0978-0.03550.04540.08-0.1172-0.2350.00820.16510.0438-0.0360.15180.03950.142723.622714.4695104.3404
43.31580.5208-0.29052.51330.77236.9974-0.14240.0587-0.3088-0.18520.04850.01140.7613-0.82610.09390.2575-0.13570.05140.20430.08040.18415.9923-0.535856.7481
58.3355-0.9742-1.39624.05060.66318.1541-0.2342-0.0997-0.9385-0.24760.1306-0.08921.2130.2740.10360.38290.07840.07210.12170.04360.298523.0436-5.110759.3286
60.9602-0.73-0.2482.7754-0.20253.92720.0293-0.19910.0162-0.18160.0287-0.283-0.20780.2908-0.0580.13830.02310.02240.19180.01540.171223.296717.581766.152
72.62330.03220.30391.63440.91445.73550.0163-0.06130.38170.50530.04590.1898-0.9119-0.628-0.06220.62040.19070.17250.14140.04790.242713.958342.574336.4236
86.9244-0.4089-0.08354.28761.6337.3460.1743-0.0180.73020.72150.0012-0.3614-0.84580.22-0.17550.5632-0.02170.06640.0094-0.00690.214530.870239.774730.8782
92.06450.5956-1.55551.6056-1.20153.9757-0.07160.2331-0.01830.20670.10840.11460.1359-0.5315-0.03680.1710.00930.0340.10310.00560.103920.441219.037225.3404
101.29820.3567-0.3054.1393-1.31022.2178-0.0166-0.1110.0630.0328-0.0412-0.0743-0.15970.10740.05780.0224-0.0201-0.03130.1640.02430.08434.276952.6498-6.0836
117.8934-0.9816-2.04275.16-1.61724.44560.1175-0.06530.44520.10720.07710.3496-0.5522-0.4529-0.19460.09290.04930.01010.23590.04270.176217.485152.2847-1.1864
120.8742-0.3878-0.7881.78250.19284.7467-0.03920.0118-0.0649-0.14330.01450.23470.3699-0.38730.02470.0578-0.0816-0.03760.20180.05430.170619.459330.6044-9.7875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 171
2X-RAY DIFFRACTION2A172 - 190
3X-RAY DIFFRACTION2A442 - 462
4X-RAY DIFFRACTION3A205 - 441
5X-RAY DIFFRACTION4B46 - 171
6X-RAY DIFFRACTION5B172 - 190
7X-RAY DIFFRACTION5B442 - 466
8X-RAY DIFFRACTION6B205 - 441
9X-RAY DIFFRACTION7C47 - 171
10X-RAY DIFFRACTION8C172 - 190
11X-RAY DIFFRACTION8C442 - 465
12X-RAY DIFFRACTION9C205 - 441
13X-RAY DIFFRACTION10D46 - 171
14X-RAY DIFFRACTION11D172 - 190
15X-RAY DIFFRACTION11D442 - 463
16X-RAY DIFFRACTION12D205 - 441

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