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- PDB-8iu7: Structure of Staphylococcus aureus NrnA (Pde2) in complex with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 8iu7
TitleStructure of Staphylococcus aureus NrnA (Pde2) in complex with Mg2+
ComponentsBifunctional oligoribonuclease and PAP phosphatase NrnA
KeywordsHYDROLASE / NanoRNase / phosphoesterase
Function / homology
Function and homology information


nucleic acid binding / Hydrolases; Acting on ester bonds / hydrolase activity
Similarity search - Function
: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsCheng, K. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
National Natural Science Foundation of China (NSFC)32270043 China
CitationJournal: To Be Published
Title: Structure of Staphylococcus aureus NrnA in complex with Mg2+.
Authors: Cheng, K. / Wang, Y.
History
DepositionMar 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
D: Bifunctional oligoribonuclease and PAP phosphatase NrnA
B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,15012
Polymers149,9564
Non-polymers1948
Water2,918162
1
A: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules

B: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0756
Polymers74,9782
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area3850 Å2
ΔGint-58 kcal/mol
Surface area27920 Å2
MethodPISA
2
C: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules

D: Bifunctional oligoribonuclease and PAP phosphatase NrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0756
Polymers74,9782
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3890 Å2
ΔGint-56 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.910, 119.670, 119.570
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Bifunctional oligoribonuclease and PAP phosphatase NrnA


Mass: 37488.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nrnA_2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A266CBU5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 3350, 0.1M magnesium formate, Tris-HCl (pH 7.5)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→59.83 Å / Num. obs: 117351 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 46.44 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.5
Reflection shellResolution: 1.86→1.91 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 8686

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→38.32 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2542 5965 5.09 %
Rwork0.2272 111314 -
obs0.2286 117279 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.78 Å2
Refinement stepCycle: LAST / Resolution: 1.86→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10143 0 8 162 10313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010710335
X-RAY DIFFRACTIONf_angle_d1.119313986
X-RAY DIFFRACTIONf_chiral_restr0.07181551
X-RAY DIFFRACTIONf_plane_restr0.01471852
X-RAY DIFFRACTIONf_dihedral_angle_d5.23441359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.47942040.41553665X-RAY DIFFRACTION99.67
1.88-1.90.44142110.41363702X-RAY DIFFRACTION99.9
1.9-1.930.4251910.39883750X-RAY DIFFRACTION99.8
1.93-1.950.41571890.38893691X-RAY DIFFRACTION99.87
1.95-1.980.38282050.37013686X-RAY DIFFRACTION99.95
1.98-20.40482000.36633675X-RAY DIFFRACTION99.82
2-2.030.41871570.35423730X-RAY DIFFRACTION99.92
2.03-2.060.33961850.33493778X-RAY DIFFRACTION99.95
2.06-2.090.33632050.31973693X-RAY DIFFRACTION99.95
2.09-2.130.32492140.30643655X-RAY DIFFRACTION99.82
2.13-2.170.3652190.30373736X-RAY DIFFRACTION99.72
2.17-2.210.28571970.29373628X-RAY DIFFRACTION99.87
2.21-2.250.32582050.27943717X-RAY DIFFRACTION99.95
2.25-2.290.30572420.27583681X-RAY DIFFRACTION99.9
2.29-2.340.30472160.28013669X-RAY DIFFRACTION99.87
2.34-2.40.3232070.2613745X-RAY DIFFRACTION99.95
2.4-2.460.28482010.26523656X-RAY DIFFRACTION99.87
2.46-2.520.31821600.27063769X-RAY DIFFRACTION99.9
2.52-2.60.28981910.27843743X-RAY DIFFRACTION99.85
2.6-2.680.33432010.2753658X-RAY DIFFRACTION99.87
2.68-2.780.28941780.26673803X-RAY DIFFRACTION99.92
2.78-2.890.31022050.27623639X-RAY DIFFRACTION99.82
2.89-3.020.30552410.27433676X-RAY DIFFRACTION99.72
3.02-3.180.28461910.26333734X-RAY DIFFRACTION99.77
3.18-3.380.29191760.24163732X-RAY DIFFRACTION99.52
3.38-3.640.25252030.22453703X-RAY DIFFRACTION99.57
3.64-4.010.23041770.20583744X-RAY DIFFRACTION99.52
4.01-4.580.17551940.17853751X-RAY DIFFRACTION99.72
4.58-5.770.18182070.17713709X-RAY DIFFRACTION99.52
5.77-38.320.21621930.16563796X-RAY DIFFRACTION99.13
Refinement TLS params.Method: refined / Origin x: 14.6144664856 Å / Origin y: -5.70125413626 Å / Origin z: 29.3042326437 Å
111213212223313233
T0.388315969921 Å2-0.030665059098 Å20.0131363199922 Å2-0.37578798926 Å2-0.00210168265226 Å2--0.417393186563 Å2
L0.144652821488 °2-0.0718096776707 °20.0392937479193 °2-0.183708736624 °20.105259072293 °2--0.23338874007 °2
S-0.0383788255392 Å °-0.0354772286591 Å °0.0382987103767 Å °0.0618982634772 Å °-0.0322907266571 Å °0.0101211222268 Å °0.0216896654029 Å °-0.0469511174434 Å °0.0721497321987 Å °
Refinement TLS groupSelection details: all

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