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- PDB-5u7v: Crystal structure of a nucleoside triphosphate diphosphohydrolase... -

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Basic information

Entry
Database: PDB / ID: 5u7v
TitleCrystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Trifolium repens in complex with AMP
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
ADENOSINE MONOPHOSPHATE / Apyrase
Similarity search - Component
Biological speciesTrifolium repens (white clover)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.5Nov 20, 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)47,3402
Polymers46,9921
Non-polymers3471
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-1 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.830, 51.910, 69.460
Angle α, β, γ (deg.)90.00, 108.46, 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.96 Å3/Da / Density % sol: 37.21 % / Description: large thick plates
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→65.9 Å / Num. obs: 19997 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.43 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.2
Reflection shellRedundancy: 3.7 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5u7p

5u7p


Resolution: 2.15→35.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.357 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26451 1030 5.2 %RANDOM
Rwork0.19544 ---
obs0.19912 18952 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.15→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 23 158 3168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193081
X-RAY DIFFRACTIONr_bond_other_d0.0010.022844
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9734200
X-RAY DIFFRACTIONr_angle_other_deg0.833.0026522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0885396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50225.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67215459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.16156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
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_it2.4743.3051592
X-RAY DIFFRACTIONr_mcbond_other2.4753.3041591
X-RAY DIFFRACTIONr_mcangle_it3.6324.9471985
X-RAY DIFFRACTIONr_mcangle_other3.6314.9491986
X-RAY DIFFRACTIONr_scbond_it2.6963.491489
X-RAY DIFFRACTIONr_scbond_other2.6953.491490
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1165.1722216
X-RAY DIFFRACTIONr_long_range_B_refined6.30527.0643749
X-RAY DIFFRACTIONr_long_range_B_other6.30527.0683750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 77 -
Rwork0.282 1371 -
obs--100 %
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)
133.628637.776944.9103
218.529721.097458.2901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 125
2X-RAY DIFFRACTION2A126 - 407

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