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- PDB-3ulj: Crystal structure of apo Lin28B cold shock domain -

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Basic information

Entry
Database: PDB / ID: 3ulj
TitleCrystal structure of apo Lin28B cold shock domain
ComponentsLin28b, DNA-binding protein
KeywordsDNA BINDING PROTEIN / beta barrel / cold shock domain fold / nucleic acid binding
Function / homology
Function and homology information


regulatory ncRNA-mediated gene silencing / nucleic acid binding / nucleolus / zinc ion binding
Similarity search - Function
: / : / Lin-28A-like, second zinc knuckle / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / zinc finger ...: / : / Lin-28A-like, second zinc knuckle / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Lin-28 homolog B
Similarity search - Component
Biological speciesXenopus tropicalis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsMayr, F. / Schuetz, A. / Doege, N. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The Lin28 cold-shock domain remodels pre-let-7 microRNA.
Authors: Mayr, F. / Schutz, A. / Doge, N. / Heinemann, U.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin28b, DNA-binding protein
B: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,44911
Polymers19,8842
Non-polymers5649
Water4,900272
1
A: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3898
Polymers9,9421
Non-polymers4467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0603
Polymers9,9421
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lin28b, DNA-binding protein
B: Lin28b, DNA-binding protein
hetero molecules

A: Lin28b, DNA-binding protein
B: Lin28b, DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,89822
Polymers39,7694
Non-polymers1,12918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2650 Å2
ΔGint-11 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.620, 52.620, 137.336
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Lin28b, DNA-binding protein


Mass: 9942.231 Da / Num. of mol.: 2 / Fragment: unp residues 27-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog)
Gene: lin28b / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: B4F6I0
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.76 Å3/Da / Density % sol: 55.29 %
Crystal growMethod: evaporation / pH: 7
Details: 2.5 M sodium acetate, 0.1 M HEPES , pH 7.0, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98141 Å / Relative weight: 1
ReflectionResolution: 1.06→32.3 Å / Num. all: 100674 / Num. obs: 100170 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 17.8
Reflection shellResolution: 1.06→1.087 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.61 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 312Z

312z


Resolution: 1.06→32.3 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.12 / SU B: 0.56 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1391 5027 5 %RANDOM
Rwork0.1196 ---
obs0.1206 100170 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.98 Å2 / Biso mean: 15.9469 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.06→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 38 272 1688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221613
X-RAY DIFFRACTIONr_bond_other_d0.0010.021199
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9882193
X-RAY DIFFRACTIONr_angle_other_deg0.87832921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3622.39471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27215283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1211515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02356
X-RAY DIFFRACTIONr_mcbond_it2.9135992
X-RAY DIFFRACTIONr_mcbond_other0.9645399
X-RAY DIFFRACTIONr_mcangle_it4.25971599
X-RAY DIFFRACTIONr_scbond_it5.0649621
X-RAY DIFFRACTIONr_scangle_it6.78311570
X-RAY DIFFRACTIONr_rigid_bond_restr1.72232812
LS refinement shellResolution: 1.06→1.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 363 -
Rwork0.226 6894 -
all-7257 -
obs--100 %

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