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- PDB-4brm: Sulfur SAD phasing of the Legionella pneumophila NTPDase1 - cryst... -

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Basic information

Entry
Database: PDB / ID: 4brm
TitleSulfur SAD phasing of the Legionella pneumophila NTPDase1 - crystal form III (closed) in complex with sulfate
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 / SAD / Resolution: 2.02 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 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 / 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 / _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 I
B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2168
Polymers83,7612
Non-polymers4556
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-104 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.966, 84.314, 102.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.987, -0.037, -0.157), (0.058, -0.99, -0.129), (-0.151, -0.137, 0.979)
Vector: 24.879, 1.017, 1.529)

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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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 3.7 / Details: 100MM NAAC PH 3.7; 300MM NA2SO4; 20% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.9
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2→32.5 Å / Num. obs: 43436 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 41.3

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Processing

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

Resolution: 2.02→32.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.28 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21639 2191 5.1 %RANDOM
Rwork0.16105 ---
obs0.16381 41185 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.02→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 22 350 6084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195961
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.948153
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.41926.046306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95515962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.333159
X-RAY DIFFRACTIONr_chiral_restr0.1340.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214651
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: 2.02→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 140 -
Rwork0.193 2494 -
obs--78.58 %
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)
11.5694-0.001-0.36970.75510.38542.0230.02120.09610.1052-0.0991-0.031-0.0336-0.1493-0.12880.00980.08610.00990.01050.0348-0.01570.029730.0836-6.4743-5.8405
23.32660.1464-1.47210.69930.21823.31570.0556-0.16680.07050.01470.1342-0.1482-0.13540.2345-0.18980.0604-0.02710.00840.0735-0.0460.046338.9796-4.24279.4397
31.153-0.41960.00321.22940.12550.57060.0544-0.0160.05230.03090.0301-0.1262-0.05390.119-0.08450.0935-0.04260.01120.0628-0.02590.023925.24775.474719.1278
42.13170.0470.0081.7284-0.88652.1910.08250.29950.0365-0.20630.13020.2574-0.0067-0.0133-0.21270.10160.0052-0.01090.08490.0540.0755-4.49368.2112-6.924
53.011.1789-0.86611.7764-1.01623.02550.06480.23440.3020.05690.19930.4274-0.0735-0.2673-0.26420.06040.02740.03550.04990.07370.1449-15.79093.38046.2014
61.1785-0.0123-0.14951.6599-0.14250.65090.0845-0.03680.04340.13740.00950.0969-0.1011-0.0102-0.0940.099-0.01820.03260.01990.00590.0237-2.7215-6.936316.5052
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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