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- PDB-2xp1: Structure of the tandem SH2 domains from Antonospora locustae tra... -

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Basic information

Entry
Database: PDB / ID: 2xp1
TitleStructure of the tandem SH2 domains from Antonospora locustae transcription elongation factor Spt6
ComponentsSPT6
KeywordsTRANSCRIPTION / IWS1 / HISTONE CHAPERONE / MRNA EXPORT
Function / homology
Function and homology information


nucleosome organization / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / histone binding
Similarity search - Function
Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / SH2 domain / SHC Adaptor Protein / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesANTONOSPORA LOCUSTAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsDiebold, M.-L. / Koch, M. / Cavarelli, J. / Romier, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Noncanonical Tandem Sh2 Enables Interaction of Elongation Factor Spt6 with RNA Polymerase II.
Authors: Diebold, M. / Loeliger, E. / Koch, M. / Winston, F. / Cavarelli, J. / Romier, C.
History
DepositionAug 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Other / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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: SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1564
Polymers20,9291
Non-polymers2283
Water36020
1
A: SPT6
hetero molecules

A: SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3138
Polymers41,8572
Non-polymers4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2390 Å2
ΔGint-91.8 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 49.776, 59.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SPT6


Mass: 20928.736 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 779-956
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANTONOSPORA LOCUSTAE (fungus) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E2QR95*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNPUBLISHED. GLY A779, SER A780 RESIDUE PROVIDED BY THE THROMBIN CLEAVAGE SITE. HIS A781, MET A782 ...UNPUBLISHED. GLY A779, SER A780 RESIDUE PROVIDED BY THE THROMBIN CLEAVAGE SITE. HIS A781, MET A782 RESIDUE PROVIDED BY THE NDEI RESTRICTION 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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growpH: 6
Details: 0.1 M MES PH 6.0, 1.5 M AMMONIUM SULFATE, 20 MM COCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. obs: 9257 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 52.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.2→32.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.802 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26559 453 4.9 %RANDOM
Rwork0.2248 ---
obs0.22678 8803 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--1.68 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 11 20 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221505
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9432028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02722.98777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0415261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.022159
X-RAY DIFFRACTIONr_chiral_restr0.1360.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211147
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_it0.6771.5873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26721416
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.063632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2374.5612
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 33 -
Rwork0.291 635 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 13.9518 Å / Origin y: 18.343 Å / Origin z: 26.5879 Å
111213212223313233
T0.0921 Å20.0519 Å2-0.0177 Å2-0.109 Å2-0.034 Å2--0.1813 Å2
L1.5772 °20.2643 °2-0.0614 °2-2.7777 °2-2.7979 °2--9.475 °2
S-0.1558 Å °0.0275 Å °-0.0481 Å °-0.2985 Å °-0.0545 Å °-0.0889 Å °0.0498 Å °0.1736 Å °0.2103 Å °

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