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- PDB-3ujm: Crystal structure of the NTF2-like domain of the Drosophila melan... -

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Basic information

Entry
Database: PDB / ID: 3ujm
TitleCrystal structure of the NTF2-like domain of the Drosophila melanogaster Rasputin protein
ComponentsRasputin
KeywordsSIGNALING PROTEIN / NTF2-like fold / Ras signaling
Function / homology
Function and homology information


compound eye photoreceptor fate commitment / negative regulation of imaginal disc growth / dorsal/ventral axis specification, ovarian follicular epithelium / ommatidial rotation / response to amino acid starvation / precatalytic spliceosome / stress granule assembly / catalytic step 2 spliceosome / cytoplasmic stress granule / ribonucleoprotein complex ...compound eye photoreceptor fate commitment / negative regulation of imaginal disc growth / dorsal/ventral axis specification, ovarian follicular epithelium / ommatidial rotation / response to amino acid starvation / precatalytic spliceosome / stress granule assembly / catalytic step 2 spliceosome / cytoplasmic stress granule / ribonucleoprotein complex / mRNA binding / positive regulation of gene expression / cytoplasm / cytosol
Similarity search - Function
Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / RNA recognition motif / RNA recognition motif ...Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.741 Å
AuthorsVognsen, T. / Kristensen, O.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster.
Authors: Vognsen, T. / Kristensen, O.
History
DepositionNov 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rasputin
B: Rasputin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2424
Polymers27,7652
Non-polymers4772
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-1 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.200, 80.380, 39.200
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rasputin


Mass: 13882.543 Da / Num. of mol.: 2 / Fragment: NTF2-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rin, CG9412 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NH72, UniProt: Q9VFT4*PLUS
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2 M diammonium phosphate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2011
RadiationMonochromator: Ge(220) and multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.74→39.16 Å / Num. all: 6272 / Num. obs: 6272 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 19.8
Reflection shellResolution: 2.74→2.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.1 / Num. unique all: 477 / Rsym value: 0.435 / % possible all: 96.6

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Processing

Software
NameVersionClassification
xia2data scaling
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q90, chain B

3q90


Resolution: 2.741→39.16 Å / SU ML: 0.77 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 290 4.64 %random
Rwork0.1965 ---
obs0.1987 6256 97.07 %-
all-6272 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.474 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.0548 Å2-0 Å2-8.5882 Å2
2---13.7506 Å20 Å2
3---5.6958 Å2
Refinement stepCycle: LAST / Resolution: 2.741→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 30 34 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022003
X-RAY DIFFRACTIONf_angle_d0.6422709
X-RAY DIFFRACTIONf_dihedral_angle_d13.11751
X-RAY DIFFRACTIONf_chiral_restr0.045279
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.741-2.810.28231370.22352966X-RAY DIFFRACTION97
3.4533-39.16360.2291530.18623000X-RAY DIFFRACTION97
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)
17.47211.3987-1.31327.49251.03415.5002-0.0304-0.5397-0.65130.16020.0117-0.6953-0.1534-0.09490.06790.29430.05440.00020.29430.00330.241112.6917-9.30069.5493
24.82320.3459-1.48924.89510.40764.6849-0.0494-0.2407-0.827-0.36070.02280.04-0.0925-0.2995-0.04460.27560.0789-0.09880.0728-0.01090.332213.8698-7.80732.1265
35.836-0.0215-1.1586.6904-1.83717.89490.13840.0958-0.30770.4035-0.1667-0.0621-0.96820.18860.07130.2675-0.0069-0.03450.2895-0.0550.286529.5998.3054-6.6645
43.8278-0.2911-1.16595.1206-0.1274.2860.01980.173-0.0745-0.00980.0230.1155-0.99120.28530.01410.3882-0.0113-0.09330.1288-0.06280.268921.89236.7521-5.2229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 14:63)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 64:130)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 14:64)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 65:130)

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