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- PDB-4xai: Crystal Structure of red flour beetle NR2E1/TLX -

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Basic information

Entry
Database: PDB / ID: 4xai
TitleCrystal Structure of red flour beetle NR2E1/TLX
Components
  • Grunge, isoform J
  • Maltose-binding periplasmic protein,Tailless ortholog
KeywordsTRANSCRIPTION / helical sandwich / TRANSPORT PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


inter-male aggressive behavior / polytene chromosome interband / imaginal disc-derived wing vein morphogenesis / imaginal disc-derived leg morphogenesis / segmentation / larval somatic muscle development / segment specification / eye development / embryonic pattern specification / histone deacetylase activity, hydrolytic mechanism ...inter-male aggressive behavior / polytene chromosome interband / imaginal disc-derived wing vein morphogenesis / imaginal disc-derived leg morphogenesis / segmentation / larval somatic muscle development / segment specification / eye development / embryonic pattern specification / histone deacetylase activity, hydrolytic mechanism / negative regulation of epidermal growth factor receptor signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / nuclear receptor binding / negative regulation of smoothened signaling pathway / transcription corepressor activity / outer membrane-bounded periplasmic space / DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Atrophin-like / Atrophin-1 family / ELM2 domain / ELM2 domain profile. / ELM2 / : / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Atrophin-like / Atrophin-1 family / ELM2 domain / ELM2 domain profile. / ELM2 / : / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / SANT/Myb domain / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Retinoid X Receptor / Retinoid X Receptor / Periplasmic binding protein-like II / Homeobox-like domain superfamily / D-Maltodextrin-Binding Protein; domain 2 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Grunge, isoform J / Maltose/maltodextrin-binding periplasmic protein / Tailless ortholog
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Tribolium castaneum (red flour beetle)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhi, X. / Zhou, E. / Xu, E.
CitationJournal: Genes Dev. / Year: 2015
Title: Structural basis for corepressor assembly by the orphan nuclear receptor TLX.
Authors: Zhi, X. / Zhou, X.E. / He, Y. / Searose-Xu, K. / Zhang, C.L. / Tsai, C.C. / Melcher, K. / Xu, H.E.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / entity_name_com / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Tailless ortholog
P: Grunge, isoform J
B: Maltose-binding periplasmic protein,Tailless ortholog
Q: Grunge, isoform J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7836
Polymers132,0984
Non-polymers6852
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-31 kcal/mol
Surface area51700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.782, 84.098, 262.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Maltose-binding periplasmic protein,Tailless ortholog / MBP / MMBP / Maltodextrin-binding protein


Mass: 63653.492 Da / Num. of mol.: 2
Fragment: maltose binding protein fused ligand binding domain,maltose binding protein fused ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Tribolium castaneum (red flour beetle)
Gene: malE, Z5632, ECs5017 / Plasmid: pETduet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEY0, UniProt: Q9NCL0
#2: Protein/peptide Grunge, isoform J


Mass: 2395.648 Da / Num. of mol.: 2 / Fragment: Atro box motif / Source method: obtained synthetically / Details: maltose / Source: (synth.) Drosophila melanogaster (fruit fly)
References: UniProt: M9PHT1, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2013
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.58→40 Å / Num. obs: 81089 / % possible obs: 92.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 11020 / Rsym value: 0.554 / % possible all: 85.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID's 4MY2 and 4LOG

4my2

4log


Resolution: 2.6→35.27 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 5590 6.94 %
Rwork0.2074 --
obs0.2111 80518 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9174 0 46 86 9306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049432
X-RAY DIFFRACTIONf_angle_d0.90812804
X-RAY DIFFRACTIONf_dihedral_angle_d13.9643466
X-RAY DIFFRACTIONf_chiral_restr0.0351443
X-RAY DIFFRACTIONf_plane_restr0.0041640
LS refinement shellResolution: 2.6→2.73 Å
RfactorNum. reflection% reflection
Rfree0.36 190 -
Rwork0.3 2535 -
obs--97 %
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)
12.5741-0.4947-0.63041.6583-0.17031.4802-0.02890.1814-0.3536-0.2055-0.1335-0.18680.33820.21620.0010.44320.0520.0480.5129-0.01390.488121.237-44.41169.0177
21.6606-0.7281-0.64260.71420.17751.393-0.1566-0.0765-0.4307-0.01930.05060.54020.3944-0.0377-0.01760.56180.0068-0.08380.58420.01560.590220.0348-21.2611-22.3238
31.34190.0424-0.34131.9445-0.07182.1533-0.0675-0.002-0.0716-0.1920.14280.169-0.0178-0.176-0.00580.5128-0.0157-0.1010.5524-0.03530.517820.5621-10.7297-33.2387
42.77810.2143-0.55961.36560.76240.62020.1197-1.00260.19570.59080.20070.2986-0.4740.48990.00960.57260.02430.03980.74020.06080.795314.0925-13.0266-7.491
53.1522-1.03981.47891.2938-0.63970.7132-0.18840.17790.04920.3929-0.2958-0.18990.0904-0.6879-0.07960.47790.04080.06860.77060.11240.56921.2415-7.3283-16.073
61.01280.11830.03511.26480.50621.8956-0.2820.2261-0.2345-0.23790.2877-0.3496-0.32840.4288-0.00710.848-0.1004-0.09960.686-0.29230.89267.7425-22.7815-86.8611
71.84930.03710.90321.6708-0.3241.088-0.38450.0298-0.0281-0.49160.04290.1935-0.4001-0.40030.01450.90740.0151-0.20570.6125-0.14150.6681-18.9654-18.4934-89.381
80.78740.76570.05350.61940.00781.5461-0.18480.3882-0.0751-0.38240.2539-0.3755-0.6690.2937-0.00881.0347-0.1078-0.10430.6452-0.14970.74971.4298-13.6627-90.2725
90.8967-0.05361.4814-0.51970.12311.413-0.1965-0.242-0.262-0.02350.13010.1308-0.2358-0.2509-0.00340.9165-0.0689-0.15040.66080.01660.7892.7136-27.5407-59.9359
101.2234-0.05160.81791.86380.70120.6425-0.064-0.0034-0.1807-0.51280.1966-0.1194-0.14180.06490.00160.8232-0.127-0.02720.6524-0.08920.555726.3414-20.4673-51.265
110.9285-0.6290.08721.15640.33930.6521-0.4343-0.1652-0.5521-0.10140.19340.4124-0.08440.1520.00480.9481-0.0055-0.17670.6217-0.07230.72327.8315-36.937-54.6271
12-0.0008-0.00220.01120.03150.03450.0264-0.40480.663-0.2921-0.368-0.17760.35340.3477-0.2363-0.04591.2159-0.2751-0.19380.73840.00680.71095.4224-38.9433-66.3651
130.61370.02140.58771.5291-0.8221.01540.10580.2749-0.42050.29330.12940.078-0.00490.2240.03631.1247-0.054-0.24450.58770.26990.90384.4824-47.2651-52.9835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 354 )
2X-RAY DIFFRACTION2chain 'A' and (resid 355 through 1290 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1291 through 1396 )
4X-RAY DIFFRACTION4chain 'P' and (resid 1814 through 1825 )
5X-RAY DIFFRACTION5chain 'P' and (resid 1826 through 1834 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 120 )
7X-RAY DIFFRACTION7chain 'B' and (resid 121 through 247 )
8X-RAY DIFFRACTION8chain 'B' and (resid 248 through 335 )
9X-RAY DIFFRACTION9chain 'B' and (resid 336 through 1289 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1290 through 1368 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1369 through 1396 )
12X-RAY DIFFRACTION12chain 'Q' and (resid 1815 through 1826 )
13X-RAY DIFFRACTION13chain 'Q' and (resid 1827 through 1832 )

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