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- PDB-5vh6: 2.6 Angstrom Resolution Crystal Structure of N-terminal Fragment ... -

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Basic information

Entry
Database: PDB / ID: 5vh6
Title2.6 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-406) of Elongation Factor G from Bacillus subtilis.
ComponentsElongation factor GEF-G
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Elongation Factor G
Function / homology
Function and homology information


ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding / cytosol
Similarity search - Function
Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like ...Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Translation factors / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.6 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-406) of Elongation Factor G from Bacillus subtilis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6323
Polymers45,5611
Non-polymers712
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 5TY0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.672, 56.672, 248.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Elongation factor G / EF-G / EF-G / Vegetative protein 19 / VEG19


Mass: 45560.898 Da / Num. of mol.: 1 / Fragment: UNP residues 1-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: fusA, fus, BSU01120 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P80868
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 8.0 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (B7), 0.2M Sodium chloride, 0.1M MES pH (6.0), 20% (w/v) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 13280 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 59.2 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rsym value: 0.093 / Χ2: 1.01 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 638 / CC1/2: 0.867 / Rpim(I) all: 0.333 / Rsym value: 0.796 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XEX

2xex


Resolution: 2.61→28.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 32.689 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 1.395 / ESU R Free: 0.36 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27732 661 5 %RANDOM
Rwork0.22542 ---
obs0.22811 12544 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.252 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å20 Å2
2--3.79 Å20 Å2
3----7.59 Å2
Refinement stepCycle: 1 / Resolution: 2.61→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 2 63 2998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192978
X-RAY DIFFRACTIONr_bond_other_d0.0010.022791
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9684033
X-RAY DIFFRACTIONr_angle_other_deg0.80936463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.575374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.04224.571140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.10215522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0921521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.023327
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02590
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_it1.8514.9621502
X-RAY DIFFRACTIONr_mcbond_other1.8444.9591501
X-RAY DIFFRACTIONr_mcangle_it3.3247.4291874
X-RAY DIFFRACTIONr_mcangle_other3.3247.4331875
X-RAY DIFFRACTIONr_scbond_it1.445.1581475
X-RAY DIFFRACTIONr_scbond_other1.4395.1621476
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6267.672160
X-RAY DIFFRACTIONr_long_range_B_refined5.61359.2653288
X-RAY DIFFRACTIONr_long_range_B_other5.61259.273285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.607→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 48 -
Rwork0.354 889 -
obs--99.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.83740.4979-1.32963.72441.78127.44610.01120.0113-0.05160.3031-0.0381-0.0081.12270.23020.02690.26980.0342-0.00330.0476-0.00880.00330.6472-27.0531-15.3566
21.56151.63670.2723.07480.735110.26440.00330.0969-0.22870.52180.3879-0.66891.40181.3041-0.39120.50930.3638-0.18060.2994-0.14050.188412.0647-27.5826-2.9368
30.3060.035-0.67471.03110.96366.40010.0155-0.10630.16710.21940.2621-0.1490.63370.2539-0.27760.24930.0306-0.03730.1986-0.07230.17962.7113-16.5951-0.5174
43.95040.3267-1.53053.27340.42396.25580.10030.3086-0.1341-0.1147-0.01240.07330.0207-0.3481-0.08790.06510.0535-0.0320.1216-0.00660.04672.8728-24.7039-33.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 95
2X-RAY DIFFRACTION2A96 - 157
3X-RAY DIFFRACTION3A158 - 300
4X-RAY DIFFRACTION4A301 - 400

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