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- PDB-7d8q: The structure of nucleotide phosphatase Sa1684 complex with GDP a... -

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Basic information

Entry
Database: PDB / ID: 7d8q
TitleThe structure of nucleotide phosphatase Sa1684 complex with GDP analogue from Staphylococcus aureus
ComponentsUPF0374 protein SAB1800c
KeywordsCYTOSOLIC PROTEIN / nucleitide 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 / FomD barrel-like fold / FomD-like / : / Domain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-GZF / Nucleoside triphosphate/diphosphate phosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 9, 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
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 SAB1800c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2424
Polymers21,7351
Non-polymers5083
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-17 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.659, 36.124, 58.924
Angle α, β, γ (deg.)90.000, 111.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0374 protein SAB1800c


Mass: 21734.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus RF122 (bacteria) / Strain: bovine RF122 / ET3-1 / Gene: SAB1800c / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YU19
#2: Chemical ChemComp-GZF / [(2R,3R,4S,5S)-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen phosphate


Mass: 459.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
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: 100 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: 1.5→50 Å / Num. obs: 30428 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.8
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1505 / CC1/2: 0.936

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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: 1.5→30.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1903 / WRfactor Rwork: 0.1672 / FOM work R set: 0.8749 / SU B: 1.216 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0679 / SU Rfree: 0.0678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1511 5 %RANDOM
Rwork0.1639 ---
obs0.165 28906 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.84 Å2 / Biso mean: 16.503 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0.88 Å2
2---1 Å20 Å2
3---1.12 Å2
Refinement stepCycle: final / Resolution: 1.5→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 30 122 1629
Biso mean--26.93 26.24 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131557
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171367
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.6742117
X-RAY DIFFRACTIONr_angle_other_deg1.6271.5953187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5475175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.922.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.766158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021708
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02338
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 114 -
Rwork0.209 2066 -
all-2180 -
obs--97.19 %

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