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- PDB-3vr1: Crystal structure analysis of the translation factor RF3 -

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Basic information

Entry
Database: PDB / ID: 3vr1
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',3'-TETRAPHOSPHATE / Peptide chain release factor 3
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionApr 3, 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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)247,8968
Polymers245,4834
Non-polymers2,4134
Water0
1
A: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9742
Polymers61,3711
Non-polymers6031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9742
Polymers61,3711
Non-polymers6031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9742
Polymers61,3711
Non-polymers6031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9742
Polymers61,3711
Non-polymers6031
Water0
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)123,9484
Polymers122,7422
Non-polymers1,2062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-19 kcal/mol
Surface area45260 Å2
MethodPISA
6
C: Peptide chain release factor 3
D: Peptide chain release factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9484
Polymers122,7422
Non-polymers1,2062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-19 kcal/mol
Surface area44910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.202, 83.461, 114.245
Angle α, β, γ (deg.)72.98, 74.18, 89.78
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 550
2114B1 - 550
3114C1 - 550
4114D1 - 550

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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-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4

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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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 8000, 0.3M NaCl, 10mM alanine, 10mM arginine, 0.1M HEPES, 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: Feb 5, 2008
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: 3→50 Å / Num. all: 54175 / Num. obs: 52309 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Num. unique allDiffraction-ID% possible all
3.02-3.125293192.5
3.12-3.245133197.4
3.24-3.374920197.3
3.37-3.565859197.3
3.56-3.795538197.1
3.79-4.075185197.2
4.07-4.515779197
4.51-5.125116196.5
5.12-6.525761194.4
6.52-505591198.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3vqt

3vqt


Resolution: 3→41.6 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.872 / SU B: 41.087 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.46
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25875 2654 5.1 %RANDOM
Rwork0.2182 ---
obs0.22025 49645 96.57 %-
all-51408 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.132 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.11 Å2-0.09 Å2
2---0.63 Å20.14 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 3→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16252 0 144 0 16396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216740
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.96922664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.952052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69823.232792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.392152856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.35115152
X-RAY DIFFRACTIONr_chiral_restr0.0910.22492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112712
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3951.510260
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.617216508
X-RAY DIFFRACTIONr_scbond_it2.536480
X-RAY DIFFRACTIONr_scangle_it4.524.56156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4064 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.330.5
Bmedium positional0.310.5
Cmedium positional0.360.5
Dmedium positional0.320.5
Amedium thermal1.72
Bmedium thermal1.792
Cmedium thermal2.022
Dmedium thermal2.232
LS refinement shellResolution: 3.004→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 196 -
Rwork0.304 3481 -
obs--91.44 %
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)
11.64870.50550.36972.61370.13492.0753-0.12570.12960.1239-0.21580.0942-0.0868-0.10060.05180.03150.0979-0.0098-0.00610.04550.00520.054719.88318.36723.501
23.8941-3.0425-0.58895.1519-8.26795.8788-0.38240.03580.13741.182-0.0617-0.34880.6244-0.55750.44410.771-0.2978-0.13160.4236-0.10850.251334.536.91814.85
32.74540.19911.18922.110.18671.817-0.08340.08960.09940.13940.0512-0.0424-0.0217-0.03160.03220.21050.05980.0264-0.0010.00760.001314.70914.32729.204
44.1919-0.0784-1.85992.0887-1.53055.6710.0323-0.25550.2623-0.0481-0.1288-0.1399-0.11010.25720.09650.13750.0394-0.0538-0.0074-0.02030.030232.313-8.96143.754
51.343-0.4310.57673.3776-0.01781.6637-0.0597-0.1338-0.20080.12220.1355-0.2062-0.00560.0149-0.07570.0842-0.03060.00690.06140.02170.042428.6614.024-8.038
6-1.29956.0633-2.00973.6527-7.1816-6.0421-0.2220.2923-0.2125-0.1981-0.0867-0.1330.4839-0.5090.30870.15160.2169-0.00510.9966-0.23190.281736.75115.6687.432
73.3695-0.5622-0.14552.39380.12840.8175-0.0499-0.0102-0.1306-0.03450.0797-0.25840.03480.013-0.02980.1795-0.05260.01640.0070.00320.034127.2218.121-15.532
81.64120.15950.55835.4596-0.65397.46070.12560.157-0.21350.1077-0.1932-0.7299-0.38840.76860.06760.0664-0.12490.07230.12840.00410.331950.05631.173-19.158
91.93980.35130.65051.91350.80571.4615-0.08650.1883-0.284-0.23960.16480.2233-0.0572-0.0251-0.07830.14130.0076-0.01290.0622-0.01380.09565.728-37.61419.487
102.59192.67450.88410.32277.54358.76110.577-0.0514-0.03760.5556-0.5496-0.19160.0203-0.1478-0.02730.17760.0867-0.02420.43270.21180.433-2.34-26.3644.387
113.51370.44970.07122.26120.0331.0347-0.0650.0067-0.15480.03720.07210.24060.0299-0.0065-0.00710.1570.03270.03730.00090.00130.03357.238-33.50527.014
122.88840.07881.26374.99861.0937.65330.0383-0.162-0.1308-0.0404-0.30880.9257-0.4198-0.74330.27050.07810.11280.07410.1111-0.0620.4015-15.383-10.31230.62
131.9064-0.68531.36120.88790.24481.4685-0.1212-0.1242-0.00960.06450.04850.0711-0.135-0.02750.07280.20050.00420.00320.0361-0.01620.02614.658-23.384-12.009
14-8.72280.39810.39886.471311.866810.7690.4585-0.2840.4539-1.2563-0.1264-0.731.1281-1.1325-0.33210.9769-0.1972-0.26361.01590.44230.1169-0.09-34.767-3.329
152.5118-0.2981.18852.1483-0.16061.978-0.0882-0.14060.0411-0.1540.06490.0303-0.0360.0150.02330.2039-0.0560.01690.0039-0.0073-0.008919.828-27.44-17.694
164.0076-1.0221-1.78822.47311.74116.12030.12710.0870.11210.0914-0.31210.1618-0.1306-0.29670.1850.1467-0.0452-0.0579-0.00410.00110.04932.007-50.542-32.215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 51
2X-RAY DIFFRACTION2A52 - 70
3X-RAY DIFFRACTION3A71 - 392
4X-RAY DIFFRACTION4A393 - 529
5X-RAY DIFFRACTION5B1 - 51
6X-RAY DIFFRACTION6B52 - 69
7X-RAY DIFFRACTION7B70 - 392
8X-RAY DIFFRACTION8B393 - 529
9X-RAY DIFFRACTION9C1 - 51
10X-RAY DIFFRACTION10C52 - 70
11X-RAY DIFFRACTION11C71 - 392
12X-RAY DIFFRACTION12C393 - 529
13X-RAY DIFFRACTION13D1 - 51
14X-RAY DIFFRACTION14D52 - 70
15X-RAY DIFFRACTION15D71 - 392
16X-RAY DIFFRACTION16D393 - 529

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