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- PDB-6b8d: 1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment... -

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Basic information

Entry
Database: PDB / ID: 6b8d
Title1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-405) of Elongation Factor G from Haemophilus influenzae
ComponentsElongation factor G
KeywordsRIBOSOMAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Elongation factor G
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / 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 factors / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation factors / 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 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionOct 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 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
Revision 1.2Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)45,2142
Polymers45,1791
Non-polymers351
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.823, 88.487, 130.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Elongation factor G / EF-G


Mass: 45178.871 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-405)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: fusA, fus, HI_0579 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: P43925
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 11.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against screen: Classics II (F6), 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350

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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: Aug 8, 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: 1.78→30 Å / Num. obs: 47575 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rsym value: 0.043 / Χ2: 1.011 / Net I/σ(I): 38.4
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2388 / CC1/2: 0.832 / Rpim(I) all: 0.325 / Rsym value: 0.797 / Χ2: 1.003 / % possible all: 100

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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 5TV2

5tv2


Resolution: 1.78→29.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.841 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21366 2357 5 %RANDOM
Rwork0.17257 ---
obs0.17457 44829 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 1.78→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 1 290 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193077
X-RAY DIFFRACTIONr_bond_other_d0.0010.022876
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9534179
X-RAY DIFFRACTIONr_angle_other_deg0.86436675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9885395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00624.653144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.89815540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5411523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0213487
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02608
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_it1.2342.6491562
X-RAY DIFFRACTIONr_mcbond_other1.2322.6481561
X-RAY DIFFRACTIONr_mcangle_it1.9873.9541963
X-RAY DIFFRACTIONr_mcangle_other1.9863.9551964
X-RAY DIFFRACTIONr_scbond_it1.5322.8991515
X-RAY DIFFRACTIONr_scbond_other1.5322.8981513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5154.2672216
X-RAY DIFFRACTIONr_long_range_B_refined5.59832.8733391
X-RAY DIFFRACTIONr_long_range_B_other5.38932.0843318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 156 -
Rwork0.233 3276 -
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)
13.6352-0.4248-0.29491.2186-0.91422.44390.01780.1953-0.3518-0.13050.0145-0.02740.28420.1033-0.03230.06650.00810.01830.037-0.05190.0912.227413.888924.4959
22.60430.3249-1.380.6514-0.02344.8231-0.07930.2261-0.171-0.09120.072-0.07580.17790.32360.00730.03430.00360.03690.0735-0.03090.069613.632317.094719.2056
33.7856-1.14331.75252.486-1.49124.39820.0170.33110.1386-0.2324-0.1605-0.59030.03580.91410.14350.0336-0.00810.07650.2237-0.0060.179528.057521.387524.2107
41.7594-0.2447-0.4271.82260.00711.6040.0272-0.25630.07690.16160.0355-0.2428-0.08940.4472-0.06270.0458-0.03830.00370.1493-0.02230.088319.604725.504836.5786
51.54530.17410.43422.06970.31884.014-0.09520.6946-0.0836-0.42560.1436-0.0389-0.0512-0.1177-0.04840.131-0.05780.03930.3426-0.03680.02487.476518.58983.013
61.74340.09060.20863.646-0.10914.3553-0.01840.6104-0.1896-0.45860.05560.02720.138-0.1917-0.03720.1115-0.0480.01570.2902-0.06750.03016.269616.44293.9283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2A64 - 106
3X-RAY DIFFRACTION3A107 - 149
4X-RAY DIFFRACTION4A150 - 295
5X-RAY DIFFRACTION5A296 - 367
6X-RAY DIFFRACTION6A368 - 405

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