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- PDB-5ty0: 2.22 Angstrom Crystal Structure of N-terminal Fragment (residues ... -

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Basic information

Entry
Database: PDB / ID: 5ty0
Title2.22 Angstrom Crystal Structure of N-terminal Fragment (residues 1-419) of Elongation Factor G from Legionella pneumophila.
ComponentsElongation factor GEF-G
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / elongation factor G / Lipid-Binding Protein
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
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
beta-D-glucopyranose / Elongation factor G
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.22 Angstrom Crystal Structure of N-terminal Fragment (residues 1-419) of Elongation Factor G from Legionella pneumophila.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_conn_angle / struct_conn / struct_keywords / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.pdbx_keywords / _struct_keywords.text
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)47,2333
Polymers47,0301
Non-polymers2032
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-10 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.399, 89.853, 117.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Elongation factor G / EF-G / EF-G


Mass: 47029.555 Da / Num. of mol.: 1 / Fragment: residues 1-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: fusA, lpg0326 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5ZYP6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.4 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: JCSG+ (C4), 0.1M HEPES (pH 6.5), 10% (w/v) PEG 6000; Cryo: Screen solution + 50% Sucrose, (1:1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.22→30 Å / Num. obs: 28863 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 24.1
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.861 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FN5

4fn5


Resolution: 2.22→29.87 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.401 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19546 1417 4.9 %RANDOM
Rwork0.16479 ---
obs0.16625 27321 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å20 Å2
2---0.99 Å20 Å2
3----1.49 Å2
Refinement stepCycle: 1 / Resolution: 2.22→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 13 218 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193125
X-RAY DIFFRACTIONr_bond_other_d0.0010.022999
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9594244
X-RAY DIFFRACTIONr_angle_other_deg0.83736922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9035396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6424.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.90815553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4041520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.023541
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02693
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_it1.983.0691560
X-RAY DIFFRACTIONr_mcbond_other1.9543.0661559
X-RAY DIFFRACTIONr_mcangle_it3.1324.5891964
X-RAY DIFFRACTIONr_mcangle_other3.1394.5921965
X-RAY DIFFRACTIONr_scbond_it2.8373.5721565
X-RAY DIFFRACTIONr_scbond_other2.8363.5721565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6315.1912281
X-RAY DIFFRACTIONr_long_range_B_refined6.92636.5393380
X-RAY DIFFRACTIONr_long_range_B_other6.75436.2053339
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 102 -
Rwork0.241 1956 -
obs--99.61 %
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)
11.9756-0.0180.40943.18221.31083.01530.0115-0.0585-0.18380.12390.0115-0.08360.36850.1068-0.0230.08570.01950.01760.0120.0120.028350.57146.86140.7
26.2707-0.9991-2.2761.1086-0.07052.9609-0.09470.3027-0.13430.05410.0245-0.03530.2925-0.30880.07030.046-0.0242-0.00220.0347-0.01090.006945.253950.324342.9242
31.8121-0.090.06072.44090.35492.35560.0090.2009-0.0287-0.4108-0.01240.01840.1027-0.06480.00340.13240.01010.00610.0281-0.00150.010450.358451.839825.7523
40.95170.0707-0.06740.9672-0.1790.71430.04180.04580.0766-0.2077-0.0008-0.1957-0.08380.1337-0.04090.13730.00830.04480.0491-0.00450.079555.578262.201532.9935
51.7442-0.3874-0.30863.0069-0.03352.5391-0.1119-0.2848-0.1990.29280.08640.1570.3126-0.09640.02540.101-0.00140.03090.05590.03260.029338.741651.360358.7895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 36
2X-RAY DIFFRACTION2A62 - 106
3X-RAY DIFFRACTION3A107 - 201
4X-RAY DIFFRACTION4A202 - 303
5X-RAY DIFFRACTION5A304 - 404

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