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- PDB-1j1j: Crystal Structure of human Translin -

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Basic information

Entry
Database: PDB / ID: 1j1j
TitleCrystal Structure of human Translin
ComponentsTranslin
KeywordsDNA BINDING PROTEIN / Testis/brain RNA binding protein / ssDNA binding protein / RNA binding protein
Function / homology
Function and homology information


endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / male germ cell nucleus / single-stranded DNA binding / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / mRNA binding ...endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / male germ cell nucleus / single-stranded DNA binding / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / mRNA binding / endoplasmic reticulum / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Translin; domain 2 / Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSugiura, I. / Sasaki, C. / Hasegawa, T. / Kohno, T. / Sugio, S. / Moriyama, H. / Kasai, M. / Matsuzaki, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of human translin at 2.2 A resolution.
Authors: Sugiura, I. / Sasaki, C. / Hasegawa, T. / Kohno, T. / Sugio, S. / Moriyama, H. / Kasai, M. / Matsuzaki, T.
History
DepositionDec 6, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translin
B: Translin
C: Translin
D: Translin


Theoretical massNumber of molelcules
Total (without water)110,5024
Polymers110,5024
Non-polymers00
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Translin

D: Translin


Theoretical massNumber of molelcules
Total (without water)55,2512
Polymers55,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3410 Å2
ΔGint-24 kcal/mol
Surface area20070 Å2
MethodPISA
3
A: Translin

C: Translin


Theoretical massNumber of molelcules
Total (without water)55,2512
Polymers55,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3390 Å2
ΔGint-23 kcal/mol
Surface area20500 Å2
MethodPISA
4
B: Translin

B: Translin


Theoretical massNumber of molelcules
Total (without water)55,2512
Polymers55,2512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3350 Å2
ΔGint-20 kcal/mol
Surface area20350 Å2
MethodPISA
5
A: Translin
B: Translin
C: Translin
D: Translin

A: Translin
B: Translin
C: Translin
D: Translin


Theoretical massNumber of molelcules
Total (without water)221,0048
Polymers221,0048
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)129.42, 135.27, 134.35
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Translin


Mass: 27625.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q15631
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.8 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Sodium Formate, Sodium Chloride, Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH7.0
3150 mM1dropNaCl
45 %(v/v)glycerol1drop
52.5 Msodium formate1reservoir
6100 mMsodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 5, 2000
RadiationMonochromator: Si III CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 57661 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 5.1 %
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 8420 / Rsym value: 0.37 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Num. obs: 57689 / % possible obs: 97.3 % / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.32 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNXrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 2899 RANDOM
Rwork0.229 --
all0.231 57238 -
obs0.231 54339 -
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 0 414 7494
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.007
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.128
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg18.16
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.73

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