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- PDB-6mew: RFXANK ankyrin repeats in complex with a RFX7 peptide -

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Basic information

Entry
Database: PDB / ID: 6mew
TitleRFXANK ankyrin repeats in complex with a RFX7 peptide
Components
  • DNA-binding protein RFXANK
  • RFX7 peptide
KeywordsDNA BINDING PROTEIN / structural genomics / ankyrin repeats / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of MHC class II biosynthetic process / intercellular bridge / RNA polymerase II core promoter sequence-specific DNA binding / histone deacetylase binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / Ras protein signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin ...positive regulation of MHC class II biosynthetic process / intercellular bridge / RNA polymerase II core promoter sequence-specific DNA binding / histone deacetylase binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / Ras protein signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA-binding, RFXANK / RFX-like DNA-binding protein / RFX DNA-binding domain / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...DNA-binding, RFXANK / RFX-like DNA-binding protein / RFX DNA-binding domain / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein RFXANK / DNA-binding protein RFX7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsTempel, W. / Xu, C. / Dong, A. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: RFXANK ankyrin repeats in complex with a RFX7 peptide
Authors: Tempel, W. / Xu, C. / Dong, A. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionSep 7, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionOct 3, 2018ID: 4QQM
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein RFXANK
B: RFX7 peptide
C: DNA-binding protein RFXANK
D: RFX7 peptide


Theoretical massNumber of molelcules
Total (without water)41,85357
Polymers41,8534
Non-polymers053
Water4,432246
1
A: DNA-binding protein RFXANK
B: RFX7 peptide


Theoretical massNumber of molelcules
Total (without water)20,92732
Polymers20,9272
Non-polymers030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-15 kcal/mol
Surface area9150 Å2
MethodPISA
2
C: DNA-binding protein RFXANK
D: RFX7 peptide


Theoretical massNumber of molelcules
Total (without water)20,92725
Polymers20,9272
Non-polymers023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-16 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.230, 29.870, 97.890
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-binding protein RFXANK / Ankyrin repeat family A protein 1 / Regulatory factor X subunit B / RFX-B / Regulatory factor X- ...Ankyrin repeat family A protein 1 / Regulatory factor X subunit B / RFX-B / Regulatory factor X-associated ankyrin-containing protein


Mass: 18926.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFXANK, ANKRA1, RFXB / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O14593
#2: Protein/peptide RFX7 peptide


Mass: 2000.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q2KHR2*PLUS
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 53 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG-3350, 0.2 M ammonium acetate, 0.1 M bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→34.71 Å / Num. obs: 35385 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Net I/σ(I): 19.5 / Num. measured all: 245359 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.816.50.4991200118580.8760.2060.5413.494.1
9.05-34.716.10.0319173130.9990.0130.03338.198.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: selected coordinates from pdb entry 3uxg

3uxg


Resolution: 1.78→34.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.786 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the structure of an isomorphous crystal was solved by molecular replacement, where ARP/WARP was subsequently used for phase improvement and automated model bulding. COOT was used for ...Details: the structure of an isomorphous crystal was solved by molecular replacement, where ARP/WARP was subsequently used for phase improvement and automated model bulding. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1957 5.6 %thin shells (sftools)
Rwork0.1759 ---
obs0.1782 33205 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.68 Å2 / Biso mean: 19.283 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å2-0.29 Å2
2--0.24 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 1.78→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 53 246 3008
Biso mean--23.22 26.22 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172613
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.6283907
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5696060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09423.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08115456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9161512
X-RAY DIFFRACTIONr_chiral_restr0.10.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
X-RAY DIFFRACTIONr_mcbond_it2.7051.9181436
X-RAY DIFFRACTIONr_mcbond_other2.7031.9181436
X-RAY DIFFRACTIONr_mcangle_it3.3972.861798
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 217 -
Rwork0.246 2272 -
all-2489 -
obs--96.36 %

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