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- PDB-5c6q: Crystal structure of the apo TOPLESS related protein 2 (TPR2) N-t... -

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Basic information

Entry
Database: PDB / ID: 5c6q
TitleCrystal structure of the apo TOPLESS related protein 2 (TPR2) N-terminal domain (1-209) from rice
ComponentsASPR2 protein
KeywordsTRANSCRIPTION / Transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression / plant development
Function / homology
Function and homology information


positive regulation of pattern recognition receptor signaling pathway / protein sequestering activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / TOPLESS, zinc finger domain / Topless family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Quinoprotein alcohol dehydrogenase-like superfamily ...: / TOPLESS, zinc finger domain / Topless family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.251 Å
AuthorsKe, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
CitationJournal: Sci Adv / Year: 2015
Title: Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors.
Authors: Ke, J. / Ma, H. / Gu, X. / Thelen, A. / Brunzelle, J.S. / Li, J. / Xu, H.E. / Melcher, K.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPR2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9692
Polymers24,9041
Non-polymers651
Water724
1
A: ASPR2 protein
hetero molecules

A: ASPR2 protein
hetero molecules

A: ASPR2 protein
hetero molecules

A: ASPR2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8768
Polymers99,6144
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area10220 Å2
ΔGint-69 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.971, 58.971, 171.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ASPR2 protein / Os01g0254100 protein / Putative CTV.2 / TOPLESS related protein 2


Mass: 24903.611 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: P0705D01.10-1, ASPR2, Os01g0254100, OsJ_01134 / Plasmid: pSumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5NBT9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M BIS-TRIS, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27821 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2014
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27821 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 10544 / Num. obs: 10544 / % possible obs: 100 % / Redundancy: 15.3 % / Net I/σ(I): 27.5
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHE

4zhe


Resolution: 3.251→34.71 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 32.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 412 4.53 %Random selection
Rwork0.2127 ---
obs0.2151 9103 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.251→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 1 4 1708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081738
X-RAY DIFFRACTIONf_angle_d1.2812337
X-RAY DIFFRACTIONf_dihedral_angle_d16.489659
X-RAY DIFFRACTIONf_chiral_restr0.05258
X-RAY DIFFRACTIONf_plane_restr0.008296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2506-3.72050.31531320.28912901X-RAY DIFFRACTION100
3.7205-4.68570.24731430.21822891X-RAY DIFFRACTION100
4.6857-34.71230.27281370.19442899X-RAY DIFFRACTION100

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