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- PDB-3vqt: Crystal structure analysis of the translation factor RF3 -

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Basic information

Entry
Database: PDB / ID: 3vqt
TitleCrystal structure analysis of the translation factor RF3
ComponentsPeptide chain release factor 3
KeywordsTRANSLATION / release factor / GTPase
Function / homology
Function and homology information


regulation of translational termination / translation release factor activity, codon specific / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Peptide chain release factor 3, domain III / Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / 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 ...Peptide chain release factor 3, domain III / Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Peptide chain release factor 3
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKihira, K. / Shomura, Y. / Shibata, N. / Kitamura, M. / Higuchi, Y.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure analysis of the translation factor RF3 (release factor 3)
Authors: Kihira, K. / Shimizu, Y. / Shomura, Y. / Shibata, N. / Kitamura, M. / Nakagawa, A. / Ueda, T. / Ochi, K. / Higuchi, Y.
History
DepositionMar 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide chain release factor 3
B: Peptide chain release factor 3
C: Peptide chain release factor 3
D: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,2568
Polymers245,4834
Non-polymers1,7734
Water17,421967
1
A: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8142
Polymers61,3711
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8142
Polymers61,3711
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8142
Polymers61,3711
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8142
Polymers61,3711
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Peptide chain release factor 3
B: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6284
Polymers122,7422
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area41640 Å2
MethodPISA
6
C: Peptide chain release factor 3
D: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6284
Polymers122,7422
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area41900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.387, 82.795, 148.293
Angle α, β, γ (deg.)104.210, 89.780, 89.630
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peptide chain release factor 3 / RF-3


Mass: 61370.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / Gene: DvMF_2372, prfC / Plasmid: pUT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8DIL5
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 336322 / Num. obs: 244843 / % possible obs: 72.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.053 / Χ2: 2.425 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.52-1.57147091.43114
1.57-1.641.2110101.221132.70.769
1.64-1.711.5169861.053150.60.52
1.71-1.81.7232181.0031690.386
1.8-1.921.8288001.074185.60.271
1.92-2.061.9315181.291193.60.163
2.06-2.271.9320371.716195.30.105
2.27-2.62323002.3771960.076
2.6-3.272322713.531960.052
3.27-502319945.2591950.037

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2h5e

2h5e


Resolution: 1.8→33.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.739 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 9597 5.1 %RANDOM
Rwork0.1769 ---
obs0.179 189405 93.54 %-
all-202485 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.68 Å2 / Biso mean: 32.1961 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.02 Å2-0.02 Å2
2--0.07 Å20.15 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 112 967 16607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02215966
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.96921614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92751954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51723.408763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.461152708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.88515139
X-RAY DIFFRACTIONr_chiral_restr0.1530.22391
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112157
X-RAY DIFFRACTIONr_mcbond_it1.2631.59789
X-RAY DIFFRACTIONr_mcangle_it2.117215765
X-RAY DIFFRACTIONr_scbond_it3.34236177
X-RAY DIFFRACTIONr_scangle_it5.2774.55849
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 628 -
Rwork0.232 11560 -
all-12188 -
obs--81.82 %
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)
10.81340.0789-0.29892.37320.19772.0327-0.0073-0.0668-0.03640.21120.0214-0.2731-0.05730.213-0.01410.01780.0025-0.01630.0433-0.01890.0578-16.4816.05928.691
21.0922-0.1431-0.29281.61790.24641.85440.04680.1732-0.0144-0.3025-0.0077-0.1750.02670.0673-0.03910.05660.01220.04250.0443-0.0320.064-18.4858.6318.061
30.8962-0.1362-0.72121.1310.7922.6510.0198-0.1585-0.00760.124-0.0102-0.0533-0.07010.0808-0.00970.0186-0.0009-0.00180.028-0.00710.0443-2519.33634.061
42.8964-0.80181.07492.1517-0.57442.85380.0497-0.1479-0.0381-0.0435-0.02670.1590.0496-0.1239-0.0230.01590.00710.00690.0279-0.01290.0057-29.364-8.29845.72
50.8787-0.15310.67041.1182-0.16582.8181-0.07290.13060.0339-0.1435-0.0535-0.1826-0.22140.24370.12640.0512-0.01510.00690.02310.01180.0277-18.697-30.7614.941
61.9122-1.24170.66992.0081-1.1753.3396-0.3037-0.22950.00340.32920.0596-0.2481-0.36940.25340.2440.114-0.001-0.06640.05140.01470.0571-13.729-29.9237.217
70.6453-0.19750.80221.0167-0.38362.55520.04860.0744-0.0401-0.1569-0.02120.02490.2191-0.0298-0.02750.043-0.00330.01540.0238-0.01160.0258-27.151-36.9468.972
82.69830.2611-0.52731.88310.1242.20230.05340.12040.1174-0.1202-0.05490.0279-0.10620.01970.00150.01230.0158-0.00120.0202-0.01610.0109-33.502-10.089-2.672
90.86310.12180.67611.82390.41332.6344-0.0632-0.13440.06290.1129-0.09640.2309-0.1795-0.27770.15960.02120.01620.00450.0369-0.03890.0354-6.696-35.872-47.049
102.46261.40930.7991.92721.16062.9846-0.34560.24880.0451-0.39280.08840.2653-0.3712-0.24020.25720.19130.0089-0.07930.093-0.02670.1281-11.642-34.835-69.429
110.87120.23650.8421.36140.21592.6680.052-0.1041-0.01190.1737-0.047-0.03070.1942-0.0166-0.0050.0461-0.00450.02340.0372-0.02630.05481.735-42.826-41.488
122.71490.0093-0.60931.6797-0.04772.4350.013-0.12140.00670.0414-0.0566-0.0461-0.0298-0.02260.04360.0008-0.01030.00970.0196-0.013-0.00258.75-15.344-29.89
130.92420.0262-0.28721.4473-0.15341.6467-0.02630.08070.0144-0.17130.01280.2128-0.0722-0.17790.01350.0374-0.0107-0.00710.0733-0.01180.075-8.15311.071-60.976
140.72590.1777-0.24891.4911-0.49531.926-0.0046-0.0873-0.05920.2139-0.01070.14650.0178-0.05730.01530.0268-0.0050.03450.0372-0.00230.0381-4.775.765-42.689
151.57330.1315-0.43061.848-0.47272.34310.00680.30510.0223-0.30540.01190.1199-0.0261-0.1743-0.01870.0565-0.0022-0.02080.0770.00160.00760.115.533-77.176
162.86980.89651.15792.25530.41552.85490.10060.1659-0.08930.0593-0.0551-0.2080.12370.1163-0.04550.0173-0.00620.00130.0203-0.00460.00964.111-13.989-78.271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 112
2X-RAY DIFFRACTION2A113 - 228
3X-RAY DIFFRACTION3A229 - 388
4X-RAY DIFFRACTION4A389 - 529
5X-RAY DIFFRACTION5B2 - 150
6X-RAY DIFFRACTION6B151 - 224
7X-RAY DIFFRACTION7B225 - 394
8X-RAY DIFFRACTION8B395 - 528
9X-RAY DIFFRACTION9C2 - 150
10X-RAY DIFFRACTION10C151 - 224
11X-RAY DIFFRACTION11C225 - 390
12X-RAY DIFFRACTION12C391 - 529
13X-RAY DIFFRACTION13D2 - 112
14X-RAY DIFFRACTION14D113 - 280
15X-RAY DIFFRACTION15D281 - 392
16X-RAY DIFFRACTION16D393 - 528

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