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- PDB-4dg7: Low resolution structure of Drosophila Translin -

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Basic information

Entry
Database: PDB / ID: 4dg7
TitleLow resolution structure of Drosophila Translin
ComponentsGM27569p
KeywordsDNA BINDING PROTEIN / translin-like fold / ssDNA/RNA binding / reductive methylation / dimethylamino-borane / formaldehyde
Function / homology
Function and homology information


behavioral response to starvation / negative regulation of circadian sleep/wake cycle, sleep / Small interfering RNA (siRNA) biogenesis / RNA metabolic process / regulatory ncRNA-mediated post-transcriptional gene silencing / single-stranded DNA binding / sequence-specific DNA binding / protein stabilization / protein homodimerization activity / RNA binding ...behavioral response to starvation / negative regulation of circadian sleep/wake cycle, sleep / Small interfering RNA (siRNA) biogenesis / RNA metabolic process / regulatory ncRNA-mediated post-transcriptional gene silencing / single-stranded DNA binding / sequence-specific DNA binding / protein stabilization / protein homodimerization activity / RNA binding / metal ion binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.195 Å
AuthorsKumar, V. / Gupta, G.D.
Citation
Journal: FEBS Open Bio / Year: 2012
Title: Low-resolution structure of Drosophila translin
Authors: Kumar, V. / Gupta, G.D.
#1: Journal: Febs J. / Year: 2008
Title: Crystal structures of Drosophila mutant translin and characterization of translin variants reveal the structural plasticity of translin proteins.
Authors: Gupta, G.D. / Makde, R.D. / Rao, B.J. / Kumar, V.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Refinement description
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GM27569p
B: GM27569p
C: GM27569p
D: GM27569p
E: GM27569p
F: GM27569p
G: GM27569p
H: GM27569p


Theoretical massNumber of molelcules
Total (without water)233,8348
Polymers233,8348
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GM27569p
B: GM27569p


Theoretical massNumber of molelcules
Total (without water)58,4582
Polymers58,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area21200 Å2
MethodPISA
3
C: GM27569p
D: GM27569p


Theoretical massNumber of molelcules
Total (without water)58,4582
Polymers58,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-16 kcal/mol
Surface area21190 Å2
MethodPISA
4
E: GM27569p
F: GM27569p


Theoretical massNumber of molelcules
Total (without water)58,4582
Polymers58,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-17 kcal/mol
Surface area21830 Å2
MethodPISA
5
G: GM27569p
H: GM27569p


Theoretical massNumber of molelcules
Total (without water)58,4582
Polymers58,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.05, 131.20, 96.40
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 8:216 )
211CHAIN B AND (RESSEQ 8:216 )
311CHAIN C AND (RESSEQ 8:216 )
411CHAIN D AND (RESSEQ 8:216 )
511CHAIN E AND (RESSEQ 8:216 )
611CHAIN F AND (RESSEQ 8:216 )
711CHAIN G AND (RESSEQ 8:216 )
811CHAIN H AND (RESSEQ 8:216 )

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Components

#1: Protein
GM27569p / Translin


Mass: 29229.221 Da / Num. of mol.: 8 / Fragment: Translin protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG11761, Dmel_CG11761, translin, trsn / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7JVK6

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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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 4000, 100mM bicine (pH 8.5), 200mM sodium formate, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2011 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 4.195→95 Å / Num. all: 16534 / Num. obs: 16416 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 121.6 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 5.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AXJ

3axj


Resolution: 4.195→48.146 Å / SU ML: 1.37 / Cross valid method: thoughout / σ(F): 0 / Phase error: 35.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 830 5.07 %RANDOM
Rwork0.2375 ---
obs0.2402 16381 99.16 %-
all-16416 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 126.406 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--33.7059 Å2-0 Å265.1542 Å2
2---44.8075 Å20 Å2
3---78.5134 Å2
Refinement stepCycle: LAST / Resolution: 4.195→48.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13931 0 0 0 13931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114155
X-RAY DIFFRACTIONf_angle_d1.27519087
X-RAY DIFFRACTIONf_dihedral_angle_d16.9375309
X-RAY DIFFRACTIONf_chiral_restr0.0832177
X-RAY DIFFRACTIONf_plane_restr0.0042427
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1707X-RAY DIFFRACTIONPOSITIONAL
12B1707X-RAY DIFFRACTIONPOSITIONAL0.064
13C1707X-RAY DIFFRACTIONPOSITIONAL0.065
14D1707X-RAY DIFFRACTIONPOSITIONAL0.054
15E1707X-RAY DIFFRACTIONPOSITIONAL0.064
16F1707X-RAY DIFFRACTIONPOSITIONAL0.063
17G1707X-RAY DIFFRACTIONPOSITIONAL0.067
18H1707X-RAY DIFFRACTIONPOSITIONAL0.068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
4.1952-4.45780.39241320.32182470247096
4.4578-4.80170.30031400.25426172617100
4.8017-5.28440.33641590.223725742574100
5.2844-6.04780.33391440.274626142614100
6.0478-7.61480.29521230.248626202620100
7.6148-48.1490.231320.19742656265699
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)
13.58160.2648-1.88522.1184-1.43546.05660.24150.0427-0.23420.1012-0.02770.2756-0.29940.0613-0.02031.0791-0.0145-0.22210.8976-0.09851.248334.915133.501919.6115
26.02751.7155-2.45233.063-0.39781.6322-0.0325-0.039-0.4460.0206-0.0723-0.1372-0.44160.0009-0.03611.32990.187-0.06731.22610.02431.189868.192529.9419-0.1691
33.82161.269-2.4894.4031-2.53273.8854-0.19760.0684-0.5171-0.1367-0.07980.04940.0482-0.0510.05381.1371-0.0759-0.08211.0738-0.16841.169939.775267.419224.782
44.96631.795-1.22752.85080.10582.7947-0.2070.4211-0.1331-0.4890.1052-0.1406-0.33980.11520.0921.5238-0.0828-0.21771.2043-0.12260.787161.859363.212-6.9794
56.48021.3084-1.19911.9304-0.66910.8644-0.2869-0.4988-0.6050.3269-0.098-0.7357-0.0061-0.03490.07721.78790.0821-0.17271.65150.12271.09665.984563.097148.143
64.2554-2.1171-2.35713.18590.23793.1680.1547-0.05490.15360.1226-0.4451-0.4030.04030.27030.15331.3981-0.1728-0.06381.3651-0.01211.56786.132875.613416.826
75.0346-3.3266-2.5371.34592.96522.65940.25030.0498-0.2578-0.2831-0.287-0.3572-0.3984-0.226-0.03721.4071-0.1349-0.14771.3418-0.01981.209457.107922.792445.6666
80.95291.1696-1.4831.2889-2.10265.64210.310.1242-0.15430.2369-0.0335-0.0873-0.3476-0.77490.04351.07520.04360.05331.189-0.12111.587488.139436.108728.2721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:218)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 8:220)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 7:218)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 7:220)
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 7:222)
6X-RAY DIFFRACTION6CHAIN F AND (RESSEQ 7:221)
7X-RAY DIFFRACTION7CHAIN G AND (RESSEQ 7:220)
8X-RAY DIFFRACTION8CHAIN H AND (RESSEQ 5:221)

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