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- PDB-8jkr: SP1746 in complex with UMP -

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Basic information

Entry
Database: PDB / ID: 8jkr
TitleSP1746 in complex with UMP
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
: / URIDINE-5'-MONOPHOSPHATE / bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
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 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,98410
Polymers25,0511
Non-polymers9329
Water2,180121
1
A: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)51,96720
Polymers50,1022
Non-polymers1,86518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5900 Å2
ΔGint-96 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.884, 69.884, 87.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#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 serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Gene: SP_1746 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H2URF8, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)

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Non-polymers , 6 types, 130 molecules

#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG4000, 0.15 M (NH4)2SO4, 0.1 M MES, 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: 0.97852 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→50.01 Å / Num. obs: 17261 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.999 / Net I/σ(I): 24.9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1266 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.663 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.302 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22526 807 4.7 %RANDOM
Rwork0.19108 ---
obs0.19279 16428 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.262 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20.8 Å20 Å2
2--1.61 Å2-0 Å2
3----5.21 Å2
Refinement stepCycle: 1 / Resolution: 2→19.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 54 121 1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191642
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9842219
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73924.44481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60515275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.319159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021221
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_it1.8824.021774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7026.019964
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7394.43866
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.11276.9537210
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 55 -
Rwork0.237 1208 -
obs--100 %

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