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- PDB-7d8i: Crystal structure of nucleoside phosphatase Sa1684 complex with A... -

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Basic information

Entry
Database: PDB / ID: 7d8i
TitleCrystal structure of nucleoside phosphatase Sa1684 complex with ATP analogue from staphylococus aureus
ComponentsUPF0374 protein SA1684
KeywordsCYTOSOLIC PROTEIN / nucleotide phosphatase
Function / homology
Function and homology information


nucleoside diphosphate phosphatase / nucleoside diphosphate phosphatase activity / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / magnesium 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Nucleoside triphosphate/diphosphate phosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsWang, Z. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971124 China
Citation
Journal: 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.
#1: Journal: J. Biol. Chem. / Year: 2016
Title: Novel Nucleoside Diphosphatase Contributes to Staphylococcus aureus Virulence
Authors: Kenta, I. / Yuki, S.
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 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,3384
Polymers21,7351
Non-polymers6033
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-16 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.298, 36.478, 56.074
Angle α, β, γ (deg.)90.000, 108.520, 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-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / 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: BL17U1 / Wavelength: 1.2809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2809 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 24142 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.05
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 1219 / CC1/2: 0.96

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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: 1.62→42.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.616 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 1248 5.2 %RANDOM
Rwork0.1773 ---
obs0.1783 22883 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.37 Å2 / Biso mean: 21.087 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.28 Å2
2---0.95 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.62→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 33 107 1617
Biso mean--22.64 32.71 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131553
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171362
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6512111
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5853172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6195173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36822.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51315267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.012158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02336
LS refinement shellResolution: 1.622→1.664 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 93 -
Rwork0.222 1646 -
all-1739 -
obs--96.77 %

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