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- PDB-3ec8: The crystal structure of the RA domain of FLJ10324 (RADIL) -

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Basic information

Entry
Database: PDB / ID: 3ec8
TitleThe crystal structure of the RA domain of FLJ10324 (RADIL)
ComponentsPutative uncharacterized protein FLJ10324
KeywordsCELL ADHESION / beta barrel / helix / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


multicellular organism development / neural crest cell migration / substrate adhesion-dependent cell spreading / GTPase binding / microtubule / signal transduction / protein-containing complex
Similarity search - Function
Rasip1/Radil, cargo-binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / FHA domain ...Rasip1/Radil, cargo-binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
LEAD (II) ION / Ras-associating and dilute domain-containing protein / Ras-associating and dilute domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsWisniewska, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Wisniewska, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Berglund, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: The crystal structure of the RA domain of FLJ10324 (RADIL)
Authors: Wisniewska, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Wisniewska, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Berglund, H.
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein FLJ10324
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1045
Polymers18,5621
Non-polymers5424
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein FLJ10324
hetero molecules

A: Putative uncharacterized protein FLJ10324
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,20810
Polymers37,1242
Non-polymers1,0848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area4910 Å2
ΔGint-25 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.080, 46.080, 135.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Putative uncharacterized protein FLJ10324


Mass: 18561.910 Da / Num. of mol.: 1 / Fragment: RA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: A4D1Z5, UniProt: Q96JH8*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pb
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.4M Ammonium dihydrogen phosphate, 0.1M TRIS pH 8.5, 35 %(v/v) MPD , VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.00849, 0.91841, 0.97968
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 27, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.008491
20.918411
30.979681
ReflectionResolution: 2.6→19.74 Å / Num. obs: 9816 / % possible obs: 99.23 %

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Processing

Software
NameVersionClassification
XDSdata scaling
autoSHARPphasing
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→11.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 26.771 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.143 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27009 524 10 %RANDOM
Rwork0.2272 ---
obs0.23149 4715 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.731 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→11.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 9 9 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221101
X-RAY DIFFRACTIONr_bond_other_d0.0010.02775
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9771481
X-RAY DIFFRACTIONr_angle_other_deg0.82431873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01223.33351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24315192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0921511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_mcbond_it0.4461.5687
X-RAY DIFFRACTIONr_mcbond_other0.0621.5282
X-RAY DIFFRACTIONr_mcangle_it0.84221091
X-RAY DIFFRACTIONr_scbond_it1.043414
X-RAY DIFFRACTIONr_scangle_it1.8434.5390
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 37 -
Rwork0.304 333 -
obs--100 %
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)
13.63531.7564-1.51476.44790.15895.8203-0.0703-0.28570.21260.12860.0502-0.0217-0.6647-0.09060.02010.11850.0418-0.04720.0624-0.02960.0687-19.35116.826-11.041
22.45560.84790.2517.78021.07565.2036-0.0651-0.14770.16390.41-0.23310.03940.6199-0.41530.29820.1258-0.08540.07070.0988-0.05820.0997-23.0542.282-11.607
30.2840.5852-0.34577.72011.79749.723-0.119-0.1060.15710.4006-0.15240.50320.2485-1.41060.27140.14120.0356-0.04810.3996-0.10950.1762-27.0877.064-18.704
43.117-0.87523.39031.73620.766712.6038-0.0558-0.01810.45260.1159-0.34770.1070.2899-0.7370.40360.118-0.01320.04440.1218-0.00770.1732-26.518-8.403-40.562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA41 - 7114 - 44
2X-RAY DIFFRACTION2AA74 - 14247 - 115
3X-RAY DIFFRACTION3AA143 - 165116 - 138
4X-RAY DIFFRACTION4AA166 - 189139 - 162

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