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- PDB-2xpl: Crystal structure of Iws1(Spn1) conserved domain from Encephalito... -

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Basic information

Entry
Database: PDB / ID: 2xpl
TitleCrystal structure of Iws1(Spn1) conserved domain from Encephalitozoon cuniculi
ComponentsIWS1
KeywordsTRANSCRIPTION / ELONGATION / RNA POLYMERASE II / MRNA EXPORT
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / nucleus
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / : / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TFIIS N-terminal domain-containing protein
Similarity search - Component
Biological speciesENCEPHALITOZOON CUNICULI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKoch, M. / Diebold, M.-L. / Cura, V. / Cavarelli, J. / Romier, C.
Citation
Journal: Embo J. / Year: 2010
Title: The Structure of an Iws1/Spt6 Complex Reveals an Interaction Domain Conserved in Tfiis, Elongin a and Med26
Authors: Diebold, M.-L. / Koch, M. / Loeliger, E. / Cura, V. / Winston, F. / Cavarelli, J. / Romier, C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and Preliminary Crystallographic Analysis of Eukaryotic Transcription and Mrna Export Factor Iws1 from Encephalitozoon Cuniculi.
Authors: Koch, M. / Diebold, M.L. / Cavarelli, J. / Romier, C.
History
DepositionAug 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: IWS1
B: IWS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4844
Polymers33,4132
Non-polymers712
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-31 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.655, 128.832, 33.644
Angle α, β, γ (deg.)90.00, 101.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IWS1


Mass: 16706.383 Da / Num. of mol.: 2 / Fragment: CONSERVED DOMAIN, RESIDUES 55-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENCEPHALITOZOON CUNICULI (fungus) / Plasmid: PNEA-TH (PET-MC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SUS7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence details51-52 PART OF THROMBIN CLEAVAGE SITE. 53-54 PART OF NDEI CLONING SITE.

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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: 2.14 Å3/Da / Density % sol: 42.65 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID PH 7.0, 20% PEG8000, 5% ETHYL ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.25→64.42 Å / Num. obs: 13209 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 15.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD STRUCTURE - UNPUBLISHED

Resolution: 2.25→64.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 17.113 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.26413 650 4.9 %RANDOM
Rwork0.20289 ---
obs0.20604 12534 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.2 Å2
2--0.47 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.25→64.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 2 54 2324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9983090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60225.43592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25115490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6991512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.51418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47622306
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6183884
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9074.5784
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.249→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 43 -
Rwork0.221 887 -
obs--98.73 %
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)
12.38690.765-1.43714.2707-0.93144.9495-0.25210.0956-0.1459-0.09710.11770.15910.4533-0.23280.13430.1214-0.02780.02290.0641-0.0330.0369-0.9471-9.27029.7403
25.33360.9943-0.84344.5364-0.67361.95710.08810.23660.5415-0.17340.06060.0534-0.0785-0.0196-0.14870.02760.0240.00260.06320.04030.12669.807420.85340.988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 194
2X-RAY DIFFRACTION2B53 - 194

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