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- PDB-8qua: GTP binding protein YsxC from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 8qua
TitleGTP binding protein YsxC from Staphylococcus aureus
ComponentsProbable GTP-binding protein EngB
KeywordsPROTEIN BINDING / YsxC / Ribosome / GTPase
Function / homology
Function and homology information


division septum assembly / GTP binding / metal ion binding
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETYL GROUP / Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBiktimirov, A. / Islamov, D. / Lazarenko, V. / Fatkhullin, B. / Validov, S. / Yusupov, M. / Usachev, K.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-74-20034 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of GTPase YsxC from Staphylococcus aureus.
Authors: Biktimirov, A. / Islamov, D. / Fatkhullin, B. / Lazarenko, V. / Validov, S. / Yusupov, M. / Usachev, K.
History
DepositionOct 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable GTP-binding protein EngB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8493
Polymers22,7131
Non-polymers1362
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-2 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.942, 55.942, 107.112
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Probable GTP-binding protein EngB


Mass: 22712.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: engB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A5ITJ8
#2: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 2.6M Potassium/sodium phosphate pH 7.6 / PH range: 6.8 - 7.4

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→20.05 Å / Num. obs: 13613 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.044 / Rrim(I) all: 0.098 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2-20.058.30.049136130.9990.0210.054
2-2.055.70.7469690.5970.4910.899

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
CrysalisProdata collection
Cootmodel building
PHASERphasing
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.046 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.245 / SU B: 5.75 / SU ML: 0.164 / Average fsc free: 0.9355 / Average fsc work: 0.9575 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3165 708 5.229 %
Rwork0.257 12831 -
all0.26 --
obs-13539 99.245 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.306 Å2
Baniso -1Baniso -2Baniso -3
1-2.787 Å2-0 Å20 Å2
2--2.787 Å20 Å2
3----5.574 Å2
Refinement stepCycle: LAST / Resolution: 2→20.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 9 32 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121517
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161477
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.8332041
X-RAY DIFFRACTIONr_angle_other_deg1.0081.7923411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1765178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.99956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53510295
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9731075
X-RAY DIFFRACTIONr_chiral_restr0.1190.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021719
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02327
X-RAY DIFFRACTIONr_nbd_refined0.1640.2258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1270.21263
X-RAY DIFFRACTIONr_nbtor_refined0.1410.2699
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0650.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.212
X-RAY DIFFRACTIONr_nbd_other0.0830.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.29
X-RAY DIFFRACTIONr_mcbond_it3.9533.656725
X-RAY DIFFRACTIONr_mcbond_other3.953.657726
X-RAY DIFFRACTIONr_mcangle_it5.6556.58898
X-RAY DIFFRACTIONr_mcangle_other5.6526.579899
X-RAY DIFFRACTIONr_scbond_it3.4043.812792
X-RAY DIFFRACTIONr_scbond_other3.4023.813793
X-RAY DIFFRACTIONr_scangle_it4.9346.9551143
X-RAY DIFFRACTIONr_scangle_other4.9326.9551144
X-RAY DIFFRACTIONr_lrange_it7.77538.6031620
X-RAY DIFFRACTIONr_lrange_other7.77338.6011618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0510.381350.3319230.3339680.9380.94998.96690.317
2.051-2.1070.402600.328780.3259410.9060.95299.68120.303
2.107-2.1670.3480.2718880.2739370.9540.96799.89330.253
2.167-2.2330.347440.2718720.2759180.9330.96399.78210.249
2.233-2.3050.329610.2797930.2828710.9510.96498.04820.252
2.305-2.3850.364290.3128080.3148440.9260.94799.17060.281
2.385-2.4740.438460.317730.3178240.8970.94599.39320.277
2.474-2.5730.367420.3257560.3278090.9340.94498.64030.282
2.573-2.6860.392300.2637400.2687730.9150.95699.61190.239
2.686-2.8140.315260.2696980.2717250.9280.95599.86210.252
2.814-2.9630.295380.2376660.247050.9480.96499.85820.225
2.963-3.1390.339540.2626050.2686610.9280.95799.69740.253
3.139-3.350.315220.2446030.2476290.9310.95999.36410.232
3.35-3.610.255290.2285590.235920.9560.96899.32430.224
3.61-3.9410.253310.235140.2315540.9610.96698.37550.231
3.941-4.3860.234190.2154650.2164990.970.97396.9940.215
4.386-5.0240.283290.1934220.1984560.9590.97698.90350.199
5.024-6.0590.31280.2533660.2573960.950.96199.49490.26
6.059-8.2020.417240.2772970.2873210.9090.9491000.275
8.202-20.0460.272130.2982050.2962190.9590.94199.54340.308

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