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- PDB-5u7x: Crystal structure of a nucleoside triphosphate diphosphohydrolase... -

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Basic information

Entry
Database: PDB / ID: 5u7x
TitleCrystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Vigna unguiculata subsp. cylindrica (Dolichos biflorus) in complex with phosphate and manganese
ComponentsNod factor binding lectin-nucleotide phosphohydrolase
KeywordsHYDROLASE / apyrase / NTPDase / RNase-H fold / mixed 5 strand beta-sheet
Function / homologyGDA1/CD39 family of nucleoside phosphatases signature. / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / carbohydrate binding / hydrolase activity / ATP binding / : / PHOSPHATE ION / Nod factor binding lectin-nucleotide phosphohydrolase
Function and homology information
Biological speciesVigna unguiculata subsp. cylindrica (catjang)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Nod factor binding lectin-nucleotide phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4094
Polymers48,1641
Non-polymers2453
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-20 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.090, 71.110, 93.270
Angle α, β, γ (deg.)90.00, 139.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nod factor binding lectin-nucleotide phosphohydrolase


Mass: 48164.277 Da / Num. of mol.: 1 / Fragment: residues 49-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna unguiculata subsp. cylindrica (catjang)
Gene: LNP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): Rosetta / References: UniProt: Q9XFC9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.88 Å3/Da / Density % sol: 57.2 % / Description: large rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M MgCl2, 50 mM acetate, pH 5.0, 9-12% MPD, 10-2-% PEG 3350, 5 mM AMP

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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: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→46.62 Å / Num. obs: 15843 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.59 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.9
Reflection shellRedundancy: 7.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

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

5u7p


Resolution: 2.6→46.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.896 / SU B: 18.473 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24804 789 5 %RANDOM
Rwork0.16796 ---
obs0.17191 15045 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.664 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 11 137 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193230
X-RAY DIFFRACTIONr_bond_other_d0.0010.022992
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9754397
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0026885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3565411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93924.61141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38815503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2891514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
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_it1.9253.0391647
X-RAY DIFFRACTIONr_mcbond_other1.9233.0381646
X-RAY DIFFRACTIONr_mcangle_it3.0194.5542057
X-RAY DIFFRACTIONr_mcangle_other3.0184.5552058
X-RAY DIFFRACTIONr_scbond_it2.5283.2641583
X-RAY DIFFRACTIONr_scbond_other2.5253.2651576
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0184.7932329
X-RAY DIFFRACTIONr_long_range_B_refined5.72424.1723687
X-RAY DIFFRACTIONr_long_range_B_other5.66824.1873655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 55 -
Rwork0.252 1103 -
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)
1-4.245418.678214.1873
2-21.659434.566512.4487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F3 - 126
2X-RAY DIFFRACTION2F127 - 414

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