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- PDB-2qva: Crystal structure of Drosophila melanogaster Translin protein -

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Basic information

Entry
Database: PDB / ID: 2qva
TitleCrystal structure of Drosophila melanogaster Translin protein
ComponentsGM27569p
KeywordsDNA BINDING PROTEIN / Translin / D. Melanogaster
Function / homology
Function and homology information


negative regulation of circadian sleep/wake cycle, sleep / behavioral response to starvation / 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 ...negative regulation of circadian sleep/wake cycle, sleep / behavioral response to starvation / 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 / identical protein binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Immunoglobulin FC, subunit C / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Immunoglobulin FC, subunit C / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGupta, G.D. / Makde, R.D. / Kumar, V.
CitationJournal: 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
DepositionAug 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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


Theoretical massNumber of molelcules
Total (without water)113,8134
Polymers113,8134
Non-polymers00
Water00
1
A: GM27569p
D: GM27569p

A: GM27569p
D: GM27569p


Theoretical massNumber of molelcules
Total (without water)113,8134
Polymers113,8134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8380 Å2
ΔGint-69 kcal/mol
Surface area34300 Å2
MethodPISA
2
B: GM27569p
C: GM27569p

B: GM27569p
C: GM27569p


Theoretical massNumber of molelcules
Total (without water)113,8134
Polymers113,8134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8840 Å2
ΔGint-65 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.580, 96.620, 153.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 4 / Auth seq-ID: 6 - 186 / Label seq-ID: 18 - 198

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
GM27569p / translin protein / CG11761-PA


Mass: 28453.352 Da / Num. of mol.: 4 / Mutation: P168S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: translin / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q7JVK6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 4000, 10% isopropanol, 5% glycerol, 100mM sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2004 / Details: Osmic mirror
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 18817 / Num. obs: 18817 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 73.2 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.8
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2268 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRX

2qrx


Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.854 / SU B: 22.564 / SU ML: 0.364 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.554 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 950 5.1 %RANDOM
Rwork0.203 ---
obs0.207 18802 90.95 %-
all-18803 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.712 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å20 Å20 Å2
2---1.86 Å20 Å2
3----2.13 Å2
Refine analyzeLuzzati coordinate error free: 0.554 Å
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5925 0 0 0 5925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226022
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9558135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97924.346306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.764151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6361540
X-RAY DIFFRACTIONr_chiral_restr0.1050.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024495
X-RAY DIFFRACTIONr_nbd_refined0.2470.22785
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.22
X-RAY DIFFRACTIONr_mcbond_it0.631.53705
X-RAY DIFFRACTIONr_mcangle_it1.1525836
X-RAY DIFFRACTIONr_scbond_it1.54232577
X-RAY DIFFRACTIONr_scangle_it2.7834.52299
Refine LS restraints NCS

Ens-ID: 1 / Number: 1468 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.370.5
2Bmedium positional0.380.5
3Cmedium positional0.360.5
4Dmedium positional0.380.5
1Amedium thermal0.752
2Bmedium thermal0.792
3Cmedium thermal0.52
4Dmedium thermal0.542
LS refinement shellResolution: 3.4→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 62 -
Rwork0.277 1051 -
obs-1051 76.5 %

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