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- PDB-8yt5: SP1746 treated with EDTA, in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8yt5
TitleSP1746 treated with EDTA, in complex with ADP
Componentsbis(5'-nucleosyl)-tetraphosphatase (symmetrical)
KeywordsHYDROLASE / enzyme / HD domain superfamily protein / phosphohydrolase / unknown gene product / SP1746
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / nucleotide binding / metal ion binding
Similarity search - Function
Ap4A hydrolase / : / HDIG domain / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJin, Y. / Niu, L. / Ke, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia.
Authors: Jin, Y. / Ke, J. / Zheng, P. / Zhang, H. / Zhu, Z. / Niu, L.
History
DepositionMar 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5904
Polymers25,0511
Non-polymers5393
Water3,621201
1
A: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules

A: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1808
Polymers50,1022
Non-polymers1,0786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area3450 Å2
ΔGint-84 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.271, 69.271, 88.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

21A-576-

HOH

31A-578-

HOH

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Components

#1: Protein bis(5'-nucleosyl)-tetraphosphatase (symmetrical)


Mass: 25051.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1746 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H2URF8, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 287.2 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350,0.2 M Potassium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98405 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98405 Å / Relative weight: 1
ReflectionResolution: 1.6→50.01 Å / Num. obs: 32997 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.9993 / Net I/σ(I): 31.97
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 2407 / CC1/2: 0.8428

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.409 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20216 1678 5.1 %RANDOM
Rwork0.19362 ---
obs0.19407 31263 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å2-0 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 1.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 29 201 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9742252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.775198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30224.21783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20315281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6241510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021258
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6631.716789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0922.567988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1171.899867
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.73433.4277486
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 111 -
Rwork0.236 2289 -
obs--100 %

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