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- PDB-8rir: S103A mutant of the BTB domain of ZBTB8A from Xenopus laevis -

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Basic information

Entry
Database: PDB / ID: 8rir
TitleS103A mutant of the BTB domain of ZBTB8A from Xenopus laevis
ComponentsZinc finger and BTB domain-containing protein 8A.1-A
KeywordsTRANSCRIPTION / Transcription regulation / BTB domain / polymerisation
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleus / metal ion binding
Similarity search - Function
: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 8A.1-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsCoste, F. / Suskiewicz, M.J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: S103A mutant of the BTB domain of ZBTB8A from Xenopus laevis
Authors: Coste, F. / Suskiewicz, M.J.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 8A.1-A
B: Zinc finger and BTB domain-containing protein 8A.1-A


Theoretical massNumber of molelcules
Total (without water)35,1482
Polymers35,1482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-23 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.149, 154.149, 154.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 57 or (resid 58...
d_2ens_1(chain "B" and (resid 5 through 32 or (resid 33...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 5 - 126 / Label seq-ID: 7 - 128

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999414292803, 0.0184922497936, 0.0287942362145), (-0.0228296235373, -0.987102730016, -0.158451912842), (0.0254927368235, -0.159016467989, 0.986946747944)Vector: -32. ...NCS oper: (Code: given
Matrix: (-0.999414292803, 0.0184922497936, 0.0287942362145), (-0.0228296235373, -0.987102730016, -0.158451912842), (0.0254927368235, -0.159016467989, 0.986946747944)
Vector: -32.912499973, 75.2463619957, 6.41520092125)

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Components

#1: Protein Zinc finger and BTB domain-containing protein 8A.1-A


Mass: 17573.959 Da / Num. of mol.: 2 / Mutation: S103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: zbtb8a.1-a, zbtb8, zbtb8.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0IH98

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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: 5.52 Å3/Da / Density % sol: 77.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: caesium chloride, MES, Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 3.72→48.75 Å / Num. obs: 7053 / % possible obs: 99.9 % / Redundancy: 19.1 % / Biso Wilson estimate: 144.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 3.72→4.16 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1944 / CC1/2: 0.786 / Rpim(I) all: 0.411 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.72→44.5 Å / SU ML: 0.5196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2897 730 10.4 %
Rwork0.2605 6289 -
obs0.2634 7019 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 142.01 Å2
Refinement stepCycle: LAST / Resolution: 3.72→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 0 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00141827
X-RAY DIFFRACTIONf_angle_d0.31812484
X-RAY DIFFRACTIONf_chiral_restr0.0342297
X-RAY DIFFRACTIONf_plane_restr0.0019320
X-RAY DIFFRACTIONf_dihedral_angle_d10.5082602
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.502810144336 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.72-4.010.34621340.35851233X-RAY DIFFRACTION99.93
4.01-4.410.27951480.30311216X-RAY DIFFRACTION100
4.41-5.040.31450.2681229X-RAY DIFFRACTION99.93
5.05-6.350.33011460.29211260X-RAY DIFFRACTION100
6.36-44.50.26551570.21971351X-RAY DIFFRACTION99.34
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)
10.9258238232811.06065855709-0.6535723733921.63421787595-0.2613769673520.785555808349-0.1726394684450.4770223917790.0177229190939-0.07172800082150.134258904867-0.276597958387-0.18343172507-0.173433754319-0.0007760974787960.672210809524-0.04257796882840.09359991846861.15310802191-0.0992429902181.27805037171-23.077670244827.6887863748-14.6582370397
20.786209792142-0.7606171790280.07090546283722.52062295857-0.5805005611920.3066379894870.007217778991850.6546399042530.4908260437760.225568233746-0.207108065235-0.188961606927-0.5501931455720.137673231909-8.26887527204E-50.797957931714-0.078337229289-0.1329200660661.30779618470.12374389051.19647655346-9.7566956650750.9813595631-12.9533738639
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 4 through 126)AA4 - 1261 - 123
22(chain 'B' and resid 5 through 126)BB5 - 1261 - 122

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