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- PDB-5u7p: Crystal structure of a nucleoside triphosphate diphosphohydrolase... -

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Basic information

Entry
Database: PDB / ID: 5u7p
TitleCrystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Trifolium repens
ComponentsApyrase
KeywordsHYDROLASE / apyrase / NTPDase / RNase-H fold / mixed 5 strand beta-sheet
Function / homology
Function and homology information


apyrase / apyrase activity / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / ATP binding / membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family
Similarity search - Domain/homology
PHOSPHATE ION / Apyrase
Similarity search - Component
Biological speciesTrifolium repens (white clover)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsCumming, M.H. / Summers, E.L. / Oulavallickal, T. / Roberts, N. / Arcus, V.L.
CitationJournal: Protein Sci. / Year: 2017
Title: Structures and kinetics for plant nucleoside triphosphate diphosphohydrolases support a domain motion catalytic mechanism.
Authors: Summers, E.L. / Cumming, M.H. / Oulavallickal, T. / Roberts, N.J. / Arcus, V.L.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title / _citation_author.name
Revision 1.3Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1823
Polymers46,9921
Non-polymers1902
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-12 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.996, 53.592, 72.835
Angle α, β, γ (deg.)90.00, 94.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apyrase


Mass: 46992.301 Da / Num. of mol.: 1 / Fragment: residues 39-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trifolium repens (white clover) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): Rosetta / References: UniProt: B9U139, apyrase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.24 Å3/Da / Density % sol: 45.1 % / Description: large thick plate
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium dihydrogen orthophosphate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.89→72.6 Å / Num. obs: 33604 / % possible obs: 99 % / Redundancy: 10.9 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 25.8
Reflection shellRedundancy: 10.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cji

3cji


Resolution: 1.89→24.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.704 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23541 1633 5.1 %RANDOM
Rwork0.1789 ---
obs0.18177 30251 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20.03 Å2
2---0.03 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.89→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 10 395 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193190
X-RAY DIFFRACTIONr_bond_other_d0.0010.022977
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.9694350
X-RAY DIFFRACTIONr_angle_other_deg0.9413.0026845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94625.224134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2315496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.293158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
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_it2.0912.0611642
X-RAY DIFFRACTIONr_mcbond_other2.092.061641
X-RAY DIFFRACTIONr_mcangle_it3.0783.0762056
X-RAY DIFFRACTIONr_mcangle_other3.0783.0772057
X-RAY DIFFRACTIONr_scbond_it2.5832.2681548
X-RAY DIFFRACTIONr_scbond_other2.5572.2541538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8243.2932282
X-RAY DIFFRACTIONr_long_range_B_refined6.41718.0593996
X-RAY DIFFRACTIONr_long_range_B_other6.26817.5893844
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 116 -
Rwork0.231 2132 -
obs--91.94 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
154.9153-8.602459.729
238.26566.641244.538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 125
2X-RAY DIFFRACTION2A126 - 412

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