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- PDB-6bk7: 1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment... -

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Basic information

Entry
Database: PDB / ID: 6bk7
Title1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis
ComponentsElongation factor GEF-G
KeywordsRIBOSOMAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Elongation factor G
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
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,9284
Polymers90,8822
Non-polymers462
Water6,810378
1
A: Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4642
Polymers45,4411
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4642
Polymers45,4411
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.450, 86.425, 75.442
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 45440.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: fusA, EF_0200 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q839G9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 12.5 mg/mL protein in 0.5 sodium chloride, 0.01 M Tris, pH 8.3 against screen PEGs II (G6), 15% w/v PEG6000, 5% w/v glycerol, cryoprotectant: reservoir

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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 2, 2017 / Details: C(111)
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 69321 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.025 / Rrim(I) all: 0.052 / Rsym value: 0.046 / Χ2: 1.004 / Net I/σ(I): 28.8
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 3419 / CC1/2: 0.774 / Rpim(I) all: 0.423 / Rrim(I) all: 0.9 / Rsym value: 0.793 / Χ2: 1.006 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VH6

5vh6


Resolution: 1.83→28.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.395 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21734 3436 5 %RANDOM
Rwork0.19145 ---
obs0.19278 65859 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.832 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å2-0.42 Å2
2---1.65 Å20 Å2
3---2.84 Å2
Refinement stepCycle: 1 / Resolution: 1.83→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 2 378 6330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196213
X-RAY DIFFRACTIONr_bond_other_d0.0010.025825
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9678452
X-RAY DIFFRACTIONr_angle_other_deg0.829313537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8735792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78825288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.891151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1151537
X-RAY DIFFRACTIONr_chiral_restr0.0840.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.026982
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021211
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_it1.5232.8963117
X-RAY DIFFRACTIONr_mcbond_other1.5222.8953116
X-RAY DIFFRACTIONr_mcangle_it2.3934.3293917
X-RAY DIFFRACTIONr_mcangle_other2.3934.3313918
X-RAY DIFFRACTIONr_scbond_it1.8593.1713096
X-RAY DIFFRACTIONr_scbond_other1.8583.1683094
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9844.6644532
X-RAY DIFFRACTIONr_long_range_B_refined5.18335.0176810
X-RAY DIFFRACTIONr_long_range_B_other5.15134.6516740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 266 -
Rwork0.301 4711 -
obs--98.03 %
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)
14.6654-2.9892-0.98493.4307-0.36672.86740.2374-0.65011.0247-0.02070.1108-0.4887-0.24610.3155-0.34820.0976-0.08580.06480.1641-0.17910.261615.91625.61139.0606
22.7755-0.1541-0.57071.39030.26613.03190.03880.34450.1556-0.1247-0.0890.188-0.2344-0.14850.05020.09120.0019-0.00860.0797-0.03360.09353.6127-0.267127.9464
33.277-0.5503-0.94152.29780.58342.416-0.0472-0.3975-0.00720.259-0.05880.4618-0.1498-0.35570.1060.07840.01990.07760.1799-0.07370.1683-6.8081-0.677845.5952
44.8133-1.3188-1.81291.53440.66981.6345-0.0937-0.51830.06610.08240.0706-0.05860.00120.24540.02320.0797-0.00720.00460.0909-0.02040.019516.4291-5.319937.5693
54.8636-0.3265-2.11511.3250.48371.8430.1099-0.33220.7278-0.03850.1301-0.2484-0.050.4897-0.240.0791-0.0385-0.00030.2119-0.06640.237232.9237-2.39730.9329
64.5068-2.81041.26893.1050.31092.73460.2302-0.6276-0.9933-0.0140.10190.48610.2528-0.333-0.33210.1189-0.093-0.05880.16950.17450.26714.552122.072176.8214
72.7587-0.08460.56711.4231-0.45752.99470.05090.3643-0.1529-0.1333-0.0926-0.19960.2460.17210.04170.0962-0.00160.0120.08950.03390.097526.851927.928165.6935
83.4039-0.60520.91762.4926-0.5612.3439-0.0424-0.3953-0.03030.2541-0.0568-0.43290.15110.33660.09910.06460.0115-0.07430.16860.07480.140637.166827.981283.311
94.8044-1.31331.76521.4654-0.65061.5867-0.0926-0.5329-0.05330.08030.06550.0493-0.0039-0.23340.02710.0801-0.0068-0.00580.09410.02030.019514.33933.17375.3979
105.0768-0.37572.02631.4474-0.48622.08740.1366-0.3324-0.74-0.06260.09630.25140.0337-0.5104-0.23290.0626-0.038-0.00630.1950.06150.2253-2.451430.031468.6655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 82
2X-RAY DIFFRACTION2A83 - 153
3X-RAY DIFFRACTION3A154 - 230
4X-RAY DIFFRACTION4A231 - 335
5X-RAY DIFFRACTION5A336 - 404
6X-RAY DIFFRACTION6B1 - 82
7X-RAY DIFFRACTION7B83 - 153
8X-RAY DIFFRACTION8B154 - 229
9X-RAY DIFFRACTION9B230 - 335
10X-RAY DIFFRACTION10B336 - 404

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