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- PDB-8rit: Dimeric mutant S103D of the BTB domain of ZBTB8A from Xenopus laevis -

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Basic information

Entry
Database: PDB / ID: 8rit
TitleDimeric mutant S103D 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 / 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: 3.75 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: Dimeric mutant S103D 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
D: Zinc finger and BTB domain-containing protein 8A.1-A
E: Zinc finger and BTB domain-containing protein 8A.1-A
G: Zinc finger and BTB domain-containing protein 8A.1-A
H: Zinc finger and BTB domain-containing protein 8A.1-A


Theoretical massNumber of molelcules
Total (without water)105,7086
Polymers105,7086
Non-polymers00
Water00
1
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)35,2362
Polymers35,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Zinc finger and BTB domain-containing protein 8A.1-A
E: Zinc finger and BTB domain-containing protein 8A.1-A


Theoretical massNumber of molelcules
Total (without water)35,2362
Polymers35,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Zinc finger and BTB domain-containing protein 8A.1-A
H: Zinc finger and BTB domain-containing protein 8A.1-A


Theoretical massNumber of molelcules
Total (without water)35,2362
Polymers35,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.993, 61.993, 71.488
Angle α, β, γ (deg.)90.000, 91.520, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 8 or (resid 9...
d_2ens_1(chain "B" and (resid 5 through 11 or (resid 12...
d_3ens_1(chain "D" and (resid 5 through 15 or (resid 16...
d_4ens_1(chain "E" and (resid 5 through 15 or (resid 16...
d_5ens_1(chain "G" and (resid 5 through 15 or (resid 16...
d_6ens_1(chain "H" and (resid 5 through 17 or (resid 18...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 5 - 123 / Label seq-ID: 7 - 125

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3DC
d_4ED
d_5GE
d_6HF

NCS oper:
IDCodeMatrixVector
1given(-0.977172207614, 0.141276163253, 0.158667962624), (0.145899402458, -0.0966248467457, 0.984569450752), (0.154427462031, 0.985243464677, 0.0738070070046)-119.767843172, -44.9334826204, 58.9418095873
2given(0.281003792353, -0.224008914164, 0.933197125509), (0.457342977494, -0.823609308115, -0.335417811877), (0.843726418705, 0.521044829129, -0.128988435209)-33.3187526282, 16.3193554986, 86.0428220226
3given(-0.15284286489, 0.981336535697, -0.116694740062), (-0.635492650894, -0.188028047958, -0.748862166116), (-0.756827687992, -0.0402995891701, 0.652370902019)-1.18146513993, -22.5218900963, -45.2756798345
4given(-0.661031725233, 0.424510692982, 0.618730740936), (0.72018176258, 0.127443586693, 0.681979736545), (0.210654425738, 0.896408837392, -0.389969113087)-92.0093643329, 14.2202893309, 37.7156850713
5given(0.822615982543, 0.462701500322, 0.330469766945), (-0.560491873785, 0.757654697421, 0.334377360024), (-0.0956650651248, -0.460289779461, 0.882599294266)6.21152166294, -37.7958807494, -48.4562373286

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Components

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


Mass: 17617.969 Da / Num. of mol.: 6 / Mutation: S103D
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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MDL MORPHEUS I 1.38 (Alcohols, Buffer 1, EDO_P8K)

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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: 3.75→129.96 Å / Num. obs: 11929 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 105.88 Å2 / CC1/2: 0.914 / Rpim(I) all: 0.129 / Net I/σ(I): 4.5
Reflection shellResolution: 3.75→3.81 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 547 / CC1/2: 0.798 / Rpim(I) all: 0.777 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.75→71.46 Å / SU ML: 0.5397 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.2488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 568 4.79 %
Rwork0.2441 11288 -
obs0.2464 11856 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 145.71 Å2
Refinement stepCycle: LAST / Resolution: 3.75→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 0 0 5226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00115328
X-RAY DIFFRACTIONf_angle_d0.30737260
X-RAY DIFFRACTIONf_chiral_restr0.0326879
X-RAY DIFFRACTIONf_plane_restr0.0019934
X-RAY DIFFRACTIONf_dihedral_angle_d8.8551715
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.461044086499
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.487260356963
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.44886146943
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.474619982028
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.622855745065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.75-4.130.32961380.30822750X-RAY DIFFRACTION97.53
4.13-4.720.28891480.25062798X-RAY DIFFRACTION99.23
4.72-5.950.33881430.28282822X-RAY DIFFRACTION99.9
5.95-71.460.26421390.2032918X-RAY DIFFRACTION99.54
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)
16.567131335152.9016188677-0.4781612715855.37756347006-0.03184471850933.35185545943-0.3876527263270.3267544223750.175820443921-0.00428343573772-0.4061554657180.6510377934520.517539540512-0.330556559953-0.001258904970231.04006995923-0.003905718953080.008010150687180.657682770652-0.1477855064081.39593183093-70.5248877587-24.547963183535.4524140277
25.186302832072.29818360032-0.8471277957824.87277804310.9894814637672.71884532685-0.4027717664220.634103832509-0.299908523635-0.788326413190.32930720078-0.7638347744210.2611685185340.2670049289559.46798986947E-51.190991683810.06741834612650.1032575759760.9570374120460.09425343111661.4235837018-48.4144058271-17.887091359626.1681945658
33.68921091541-1.24451192836-1.364343014181.075297075281.757076428063.044811975490.1021811087950.6453663805810.120640165828-0.383951336453-0.136674184701-0.0603091244843-0.03649323799830.838277862280.0003046356946731.41968773699-0.228143422329-0.06182222958542.094036251280.2444856435431.25601358088-14.6430468988-7.598234447748.86877620303
44.44611860455-0.8933026356781.535238014822.319945495170.7707222827314.06731329935-0.120163789508-0.8259484899010.4491995120620.306623792980.3623044991830.0828423344901-0.1825076514111.60135608714-0.0003349558376861.2111589031-0.328713769456-0.04720136071271.720079799950.07943395814481.36326249345-18.72220010490.29625324949132.5283624582
53.63877345618-0.504917442216-0.2713378369480.630694116498-0.1316806225961.53268412419-0.6409014334351.08099079252-0.416691274229-0.2609635214540.5672784664630.2853365209110.8175936770190.316930755871-0.0002430344047211.596806663270.100718580526-0.1111851007251.862096352380.07231432951681.23624912922-33.407906168-15.6444274823-13.2268376857
62.25574903165-0.655883649474-1.980827726422.518616722980.6368684154323.960542728090.2055162860680.5773634961290.09901520885660.582036659172-0.1057352254470.1523675061060.325529226322-0.9828226762070.0001065393270251.506183921560.0616991076716-0.1041619485381.961264901640.3600336593841.43603276879-51.5296385728-4.992439931121.02609983766
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 3 through 123)AA3 - 1231 - 121
22(chain 'B' and resid 5 through 123)BB5 - 1231 - 119
33(chain 'D' and resid 4 through 123)DC4 - 1231 - 120
44(chain 'E' and resid 4 through 124)ED4 - 1241 - 121
55(chain 'G' and resid 4 through 124)GE4 - 1241 - 121
66(chain 'H' and resid 3 through 123)HF3 - 1231 - 121

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