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- PDB-7d8l: The structure of nucleoside phosphatase Sa1684 complex with GTP a... -

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Basic information

Entry
Database: PDB / ID: 7d8l
TitleThe structure of nucleoside phosphatase Sa1684 complex with GTP analogue from Staphylococcus aureus
ComponentsUPF0374 protein SA1684
KeywordsCYTOSOLIC PROTEIN / nucleotide phosphatase
Function / homology
Function and homology information


nucleoside diphosphate phosphatase / nucleoside-triphosphate phosphatase / hydrolase activity / metal ion binding
Similarity search - Function
Uncharacterised protein family UPF0374 / Domain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402)
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Nucleoside triphosphate/diphosphate phosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsWang, Z. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971124 China
CitationJournal: Febs J. / Year: 2021
Title: The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus.
Authors: Wang, Z. / Shen, H. / He, B. / Teng, M. / Guo, Q. / Li, X.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0374 protein SA1684
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4155
Polymers21,7351
Non-polymers6804
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-15 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.968, 35.907, 59.460
Angle α, β, γ (deg.)90.000, 111.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0374 protein SA1684


Mass: 21734.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Strain: N315 / Gene: SA1684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A4T2
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG400, 0.1M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 28764 / % possible obs: 98.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.53
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 1401 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→45.54 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.097 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1405 5.1 %RANDOM
Rwork0.2166 ---
obs0.2184 26411 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.89 Å2 / Biso mean: 17.48 Å2 / Biso min: 9.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0.68 Å2
2---0.98 Å2-0 Å2
3---1.06 Å2
Refinement stepCycle: final / Resolution: 1.55→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 40 133 1650
Biso mean--17.53 27.16 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171372
X-RAY DIFFRACTIONr_angle_refined_deg1.651.652132
X-RAY DIFFRACTIONr_angle_other_deg1.4071.5853197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5575175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31123.04392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27915268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.192158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
LS refinement shellResolution: 1.55→1.589 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.254 94 -
Rwork0.241 1819 -
obs--92.37 %

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