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- PDB-4bro: Legionella pneumophila NTPDase1 crystal form IV (part-open) -

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Basic information

Entry
Database: PDB / ID: 4bro
TitleLegionella pneumophila NTPDase1 crystal form IV (part-open)
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: 1.99 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 1.2Dec 25, 2013Group: Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I


Theoretical massNumber of molelcules
Total (without water)83,7612
Polymers83,7612
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-6.2 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.991, 155.991, 79.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.912, 0.368, 0.18), (0.363, -0.93, 0.058), (0.188, 0.012, -0.982)
Vector: 4.348, -11.892, -18.825)

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 7.5 / Details: 100MM HEPES PH 7.5, 1.4 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.837
11K, H, -L20.163
ReflectionResolution: 2→34 Å / Num. obs: 74335 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→34.17 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.884 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24069 1441 1.9 %RANDOM
Rwork0.2146 ---
obs0.21509 72874 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.104 Å2
Baniso -1Baniso -2Baniso -3
1-10.28 Å20 Å20 Å2
2--10.28 Å20 Å2
3----20.56 Å2
Refinement stepCycle: LAST / Resolution: 1.99→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 0 103 5673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9377901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.12426.088294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60415921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.835158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214510
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: 1.993→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 102 -
Rwork0.245 4738 -
obs--88.1 %
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)
11.5961-0.0228-0.14281.5255-0.34931.9225-0.0018-0.06760.07690.0226-0.00020.0370.1390.01840.00210.0883-0.019-0.01550.0138-0.01910.1829-81.7397-13.84720.534
23.879-1.0991-0.06482.4754-0.02952.1833-0.0876-0.2612-0.00220.2782-0.0383-0.01440.0590.15440.12590.15520.0285-0.01310.0455-0.01910.1611-68.6499-14.617211.1239
30.9581-0.7153-0.06441.86170.44741.1159-0.003-0.14430.12980.07630.0187-0.11230.03140.1246-0.01580.06760.0157-0.01970.0620.01290.1895-54.8805-23.6764-1.0422
41.96130.889-0.43061.3237-0.00440.1487-0.0550.3250.1348-0.27440.05940.1232-0.0197-0.0749-0.00440.24480.0156-0.0040.16870.0440.2142-75.5014-29.4962-34.2576
51.45861.0629-0.58252.8069-0.24.1615-0.19540.21880.1633-0.35720.09790.0870.2355-0.2770.09750.29920.01330.03740.21990.07030.2149-61.4676-23.1408-43.0747
60.981-0.5113-0.31321.64740.1811.30060.01570.11770.0897-0.1618-0.0812-0.1425-0.00870.32050.06550.14020.00680.03520.13050.08830.2702-54.9785-10.6733-28.8378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 155
2X-RAY DIFFRACTION2A156 - 179
3X-RAY DIFFRACTION2A377 - 394
4X-RAY DIFFRACTION3A180 - 376
5X-RAY DIFFRACTION4B34 - 155
6X-RAY DIFFRACTION5B156 - 179
7X-RAY DIFFRACTION5B377 - 394
8X-RAY DIFFRACTION6B180 - 376

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