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- PDB-4bvo: Legionella pneumophila NTPDase1 crystal form VI (part-open) in co... -

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Basic information

Entry
Database: PDB / ID: 4bvo
TitleLegionella pneumophila NTPDase1 crystal form VI (part-open) in complex with polytungstate POM-1
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
KeywordsHYDROLASE / APYRASE / ATPASE / PURINERGIC SIGNALLING / TWINNING / METAL CLUSTER / KEGGIN
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
12-POLYTUNGSTATE / L(+)-TARTARIC ACID / Ectonucleoside triphosphate diphosphohydrolase I
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsZebisch, M. / Schaefer, P. / Straeter, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of Legionella Pneumophila Ntpdase1 in Complex with Polyoxometallates.
Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Strater, N.
History
DepositionJun 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Nov 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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5815
Polymers41,5371
Non-polymers3,0444
Water3,657203
1
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules

A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,16310
Polymers83,0742
Non-polymers6,0888
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4140 Å2
ΔGint-35.6 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.692, 143.692, 75.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1397-

NA

21A-2117-

HOH

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Components

#1: Protein ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I / NTPDASE1


Mass: 41537.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-393
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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-E43 / 12-POLYTUNGSTATE


Mass: 2848.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O40W12
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 0.54 % / Description: NONE
Crystal growDetails: 100MM TRIS PH 7.3, 200MM K NA TARTRATE, 18% PEG3350, 10MM POM1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9181
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.7→29.4 Å / Num. obs: 50327 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 14.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→124.44 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.195 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19757 1293 2.6 %RANDOM
Rwork0.14907 ---
obs0.15036 49027 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→124.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 64 203 3107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.984216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15625.96151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.415487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.207155
X-RAY DIFFRACTIONr_chiral_restr0.090.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212341
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_it2.8312.0431445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6253.0771810
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3012.5251617
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.29318.6844783
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.91133062
X-RAY DIFFRACTIONr_sphericity_free28.903574
X-RAY DIFFRACTIONr_sphericity_bonded18.47953090
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 82 -
Rwork0.233 3389 -
obs--93.79 %

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