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- PDB-8p2n: Polymeric form of the BTB domain of ZBTB8A from Xenopus laevis -

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Basic information

Entry
Database: PDB / ID: 8p2n
TitlePolymeric form 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: 3.1 Å
AuthorsCoste, F. / Mance, L. / Suskiewicz, M.J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Polymeric form of the BTB domain of ZBTB8A from Xenopus laevis
Authors: Coste, F. / Mance, L. / Suskiewicz, M.J.
History
DepositionMay 16, 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)35,1802
Polymers35,1802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-22 kcal/mol
Surface area11920 Å2
Unit cell
Length a, b, c (Å)153.695, 153.695, 153.695
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 7 through 73 or (resid 74...
d_2ens_1(chain "B" and (resid 7 through 75 or (resid 76...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISGLUA5 - 124
d_21ens_1HISGLUB3 - 122

NCS oper: (Code: givenMatrix: (-0.986145738629, 0.0216188880639, -0.164466427769), (-0.0173813997273, -0.999479951708, -0.0271608740227), (-0.164968085179, -0.0239259234522, 0.986008661757)Vector: ...NCS oper: (Code: given
Matrix: (-0.986145738629, 0.0216188880639, -0.164466427769), (-0.0173813997273, -0.999479951708, -0.0271608740227), (-0.164968085179, -0.0239259234522, 0.986008661757)
Vector: 169.598158941, 113.849004863, 15.4858466565)

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Components

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


Mass: 17589.959 Da / Num. of mol.: 2
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: 4.3 Å3/Da / Density % sol: 71.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: PEG200, Na/K phosphate, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.1→48.6 Å / Num. obs: 11832 / % possible obs: 100 % / Redundancy: 65.3 % / Biso Wilson estimate: 130.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 16
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 66.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2074 / CC1/2: 0.63 / Rpim(I) all: 0.751 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXv1.20refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.6 Å / SU ML: 0.5952 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 1125 9.55 %
Rwork0.2378 10655 -
obs0.2401 11780 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.18 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 0 0 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171850
X-RAY DIFFRACTIONf_angle_d0.37432508
X-RAY DIFFRACTIONf_chiral_restr0.036298
X-RAY DIFFRACTIONf_plane_restr0.0025319
X-RAY DIFFRACTIONf_dihedral_angle_d11.6866619
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.446202024908 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.53041370.47281293X-RAY DIFFRACTION99.31
3.24-3.410.33971420.34771279X-RAY DIFFRACTION99.93
3.41-3.630.32981510.29591296X-RAY DIFFRACTION99.93
3.63-3.910.37411240.30471319X-RAY DIFFRACTION100
3.91-4.30.29381360.23411317X-RAY DIFFRACTION100
4.3-4.920.23071470.2131331X-RAY DIFFRACTION100
4.92-6.190.27911470.23951348X-RAY DIFFRACTION100
6.2-48.60.2031410.20081472X-RAY DIFFRACTION99.63
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)
12.612386486160.5558924188870.9824157397590.2439985823210.5529198207090.945832656443-0.097211085886-0.294025176581-0.8397011518950.531301332027-0.1411335908290.2878452878880.907809579978-0.446432710417-0.0002388911328951.13750275486-0.06141119902270.06380890862930.71312788526-0.008951533929231.3047877122770.691821301152.2226575254101.70718122
22.37512419501-0.356911467476-0.217716705622.43645896863-0.9501693448430.9295824945420.0861298677566-0.753691961570.6546454851480.620742267947-0.3923008564410.5173253696680.106697197128-0.353823453935-0.0004861645327881.004652763190.04857270779880.05730628050280.825106612605-0.07109344166151.2893270129467.875460173862.4610880373106.733116004
31.37360990469-0.8351559034671.097301198030.45529035203-0.5367999846270.8091545939580.4310600877610.1469334052-0.240561149580.241158577131-0.3295428245340.1477746515570.37086974823-0.3788388054162.00863457053E-51.162498560440.189797364412-0.2016375263870.868542543891-0.02192899163741.1953447380960.910002246168.02227309491.2288176736
40.475514256517-0.116931694883-0.1767832479480.2063046908570.1451281301190.0997853023512-0.4551351812230.5857795795481.16310221962-0.150415843763-1.13901101262-0.388198315356-1.332148710690.790822996079-0.005498521788941.30357674777-0.122910492564-0.03793882524181.12158006290.01085407182341.4552642610781.821404263460.360583603598.6955764045
50.297136807621-0.02783746828930.4171574264580.09319966196170.1154436601930.7803462398520.118755949408-1.60507119799-0.8360361978750.0410997498949-0.2774071847561.39439605625-0.2255459698880.0537619868033-0.001836370102061.316587627940.0935985025161-0.06812657463411.08058545688-0.05607667715851.2132098992188.626395192253.9832093408111.65797011
61.43183620595-0.572602279691-0.4399239071610.314406520972-0.1364194377081.328279054740.0664669474309-0.0598988271211-0.15396296698-0.245733221008-0.047108552419-0.3033310353040.396987557510.2401269274244.94431982047E-51.017854303010.00439035347597-0.01591960235550.763349639360.1528564838941.1597103841282.871221803246.5446371271108.127425936
70.126863466417-0.08789141435450.3213832311280.773655377620.5170885857991.69424174824-0.501368820697-0.811079039177-0.2634353807221.35994570468-0.174943736021-0.4959868696590.4657030331660.16565103503-0.0007957894466981.360955914380.115511055062-0.03773937006260.9563774429930.09843409145131.2043294333486.970402620646.5617072616113.361997259
80.253500364403-0.148156351301-0.2218146633960.0694583644970.1299329857660.178926482121-0.6995283382640.2186204637521.046771900220.006156877731440.643500048027-0.781025494565-0.9486290297380.509113022475-0.001774124391821.249941219310.1174516398980.02715306099960.7351610314360.08281944431651.1410713604392.993342146450.9214969797.852295328
9-0.00848199355481-0.0139167875481-0.03140584858260.1231605646640.2012932399940.294061547650.6887765090630.0949799540840.1155250461591.071721708720.3963901773140.884878208214-1.794758332590.7696139976410.007850202140141.01913475541-0.01547396989230.1774762160261.124801716490.2600734482261.1248541905898.070773551441.267940589597.9179054768
100.304664864148-0.2274834710950.3523558079264.293794087121.012295865580.7921126922410.3130768902560.3630371901440.504256527596-0.471524573536-0.407230440604-0.970436518124-0.06078003382150.0547314375488-0.1837570223661.526987741440.4770068759270.2514897267570.7015795550940.1125648182351.1214911618892.195399077340.658387977192.5542964006
111.027254310011.169077031341.727054736331.464472364491.972850883142.91389197476-0.433440688920.03458503917940.103497614256-1.107308416911.05360468345-0.838478154829-1.417772285351.27627127713-0.136264487580.887209819750.3174256290160.4479233639721.620725235720.3302772915611.39130813814107.22441685535.300403708786.2102006055
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 32 )AA3 - 321 - 30
22chain 'A' and (resid 33 through 83 )AA33 - 8331 - 81
33chain 'A' and (resid 84 through 126 )AA84 - 12682 - 124
44chain 'B' and (resid 5 through 20 )BB5 - 201 - 16
55chain 'B' and (resid 21 through 32 )BB21 - 3217 - 28
66chain 'B' and (resid 33 through 57 )BB33 - 5729 - 53
77chain 'B' and (resid 58 through 72 )BB58 - 7254 - 68
88chain 'B' and (resid 73 through 91 )BB73 - 9169 - 87
99chain 'B' and (resid 92 through 104 )BB92 - 10488 - 100
1010chain 'B' and (resid 105 through 119 )BB105 - 119101 - 115
1111chain 'B' and (resid 120 through 126 )BB120 - 126116 - 122

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