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- PDB-6n0i: 2.60 Angstrom Resolution Crystal Structure of Elongation Factor G... -

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Basic information

Entry
Database: PDB / ID: 6n0i
Title2.60 Angstrom Resolution Crystal Structure of Elongation Factor G 2 from Pseudomonas putida.
ComponentsElongation factor G 2EF-G
KeywordsTRANSLATION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Elongation Factor G 2
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / 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 / Ribosomal Protein S5; domain 2 / 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 / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Elongation factor G 2
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMinasov, G. / Shuvalova, L. / Wawrzak, Z. / Cardona-Correa, A. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.60 Angstrom Resolution Crystal Structure of Elongation Factor G 2 from Pseudomonas putida.
Authors: Minasov, G. / Shuvalova, L. / Wawrzak, Z. / Cardona-Correa, A. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor G 2
B: Elongation factor G 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,7045
Polymers156,4062
Non-polymers2983
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, 4fn5
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-13 kcal/mol
Surface area61810 Å2
Unit cell
Length a, b, c (Å)49.434, 79.968, 183.516
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 701 / Label seq-ID: 4 - 704

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Elongation factor G 2 / EF-G / EF-G 2


Mass: 78202.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: fusB, fusA-2, PP_4111 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q88FI4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 9.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (C10), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.0), 20% (w/v) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 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: 44241 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 65.9 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.041 / Rsym value: 0.078 / Χ2: 1.009 / Net I/σ(I): 17.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2141 / CC1/2: 0.742 / Rpim(I) all: 0.427 / Rrim(I) all: 0.912 / Rsym value: 0.804 / Χ2: 0.994 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FN5

4fn5


Resolution: 2.6→29.83 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 34.051 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.351 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26393 2120 4.8 %RANDOM
Rwork0.22316 ---
obs0.22517 41967 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.367 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å21.04 Å2
2--4.46 Å20 Å2
3----2.53 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10509 0 17 116 10642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01310709
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710097
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.64614456
X-RAY DIFFRACTIONr_angle_other_deg0.2921.57823417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.47851349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.59822.151581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.857151903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.3271584
X-RAY DIFFRACTIONr_chiral_restr0.0490.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.0212059
X-RAY DIFFRACTIONr_gen_planes_other0.0490.022205
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_it2.4264.4845408
X-RAY DIFFRACTIONr_mcbond_other2.4254.4845407
X-RAY DIFFRACTIONr_mcangle_it4.0346.7246753
X-RAY DIFFRACTIONr_mcangle_other4.0346.7256754
X-RAY DIFFRACTIONr_scbond_it2.7084.8115301
X-RAY DIFFRACTIONr_scbond_other2.7084.8125302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4257.0867704
X-RAY DIFFRACTIONr_long_range_B_refined7.09152.98611585
X-RAY DIFFRACTIONr_long_range_B_other7.08452.97611582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19278 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 168 -
Rwork0.357 3006 -
obs--100 %
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)
13.8986-0.34730.76033.96510.16175.11710.09760.0365-0.01150.5546-0.05070.11570.3597-0.6868-0.04690.1651-0.0747-0.01560.16390.10960.1686-0.7976-10.561323.0402
23.25071.3408-1.82373.65630.38353.95420.4129-0.32850.5850.70530.0612-0.1125-0.7776-0.4106-0.47410.69030.07530.05910.2776-0.01720.49874.12597.834230.3973
32.3492-0.5625-1.31344.67160.85213.2255-0.01180.37180.1351-0.2622-0.1130.37940.1814-0.72960.12480.23-0.0718-0.05980.34390.12440.1667-1.0373-16.216413.0465
48.76990.08521.30852.40750.24153.14250.1285-0.059-0.7228-0.1770.1541-0.0020.11140.0353-0.28260.0194-0.0139-0.01940.0515-0.00160.11933.2664-41.431529.7704
50.8457-1.6091-2.29164.06134.36157.3723-0.1499-0.24710.1024-0.0460.4033-0.1810.43520.7123-0.25340.15170.01730.01370.2116-0.15110.153727.2956-52.508711.0189
63.7488-0.19690.78263.25051.49696.5087-0.26010.35240.152-0.00450.06930.0108-0.4445-0.09160.19080.08760.0004-0.06250.0907-0.00040.050223.3697-29.186839.037
73.86141.63690.01385.6622-0.7623.3771-0.0283-0.0132-0.054-0.711-0.0651-0.7214-0.15460.01610.09340.18040.03580.04330.2718-0.13330.203524.4392-9.012770.5608
80.9731-0.2605-0.15833.9657-0.70311.7292-0.10270.18110.2825-0.93050.04630.082-0.4357-0.21360.05640.52180.0117-0.12390.3135-0.11680.202815.52894.332565.7534
93.7531-0.0411-1.35761.69631.11153.8013-0.1218-0.528-0.13920.1696-0.04640.01080.37440.33780.16820.07580.0051-0.01220.411-0.04550.056116.1923-25.44980.1011
107.53820.54021.59621.7782-0.85222.12980.0286-0.2226-0.4755-0.07880.0803-0.03880.2428-0.2299-0.10890.05010.0296-0.01080.2026-0.00970.033511.7933-39.844358.2539
112.4540.28241.25373.3581-4.49888.119-0.1717-0.0710.28060.25750.44070.0933-0.5038-1.0828-0.2690.06450.15030.00770.55270.17660.1445-8.2881-50.91182.2838
125.9007-1.27420.2992.6642-1.71455.0960.1527-0.50420.2902-0.23760.0986-0.0118-0.07220.1531-0.25120.052-0.0545-0.01570.30510.00330.0864-8.7331-31.873449.8961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 137
2X-RAY DIFFRACTION2A138 - 241
3X-RAY DIFFRACTION3A242 - 407
4X-RAY DIFFRACTION4A408 - 486
5X-RAY DIFFRACTION5A487 - 608
6X-RAY DIFFRACTION6A609 - 702
7X-RAY DIFFRACTION7B0 - 96
8X-RAY DIFFRACTION8B97 - 297
9X-RAY DIFFRACTION9B298 - 409
10X-RAY DIFFRACTION10B410 - 491
11X-RAY DIFFRACTION11B492 - 607
12X-RAY DIFFRACTION12B608 - 701

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