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- PDB-8p2o: Dimeric mutant S103R of the BTB domain of ZBTB8A from Xenopus laevis -

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Basic information

Entry
Database: PDB / ID: 8p2o
TitleDimeric mutant S103R 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: 1.85 Å
AuthorsCoste, F. / Mance, L. / Pukalo, Z. / Suskiewicz, M.J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Dimeric mutant S103R of the BTB domain of ZBTB8A from Xenopus laevis
Authors: Coste, F. / Mance, L. / Pukalo, Z. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81710
Polymers35,3202
Non-polymers4978
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint4 kcal/mol
Surface area12010 Å2
Unit cell
Length a, b, c (Å)87.918, 87.918, 97.795
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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


Mass: 17660.076 Da / Num. of mol.: 2 / Mutation: S103R
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG8000, Na Citrate

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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: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→48.9 Å / Num. obs: 36642 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 35.29 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.044 / Net I/σ(I): 9.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2244 / CC1/2: 0.801 / Rpim(I) all: 0.432 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.48 Å / SU ML: 0.1593 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1881 1781 4.87 %
Rwork0.1694 34786 -
obs0.1703 36567 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.83 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 32 185 2106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681989
X-RAY DIFFRACTIONf_angle_d0.74132669
X-RAY DIFFRACTIONf_chiral_restr0.0494303
X-RAY DIFFRACTIONf_plane_restr0.0057340
X-RAY DIFFRACTIONf_dihedral_angle_d12.2545731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.23841450.24322679X-RAY DIFFRACTION99.79
1.9-1.960.27881490.24782654X-RAY DIFFRACTION99.68
1.96-2.020.24781360.2062620X-RAY DIFFRACTION99.93
2.02-2.090.22471430.18272675X-RAY DIFFRACTION100
2.09-2.170.20921220.17232686X-RAY DIFFRACTION99.93
2.18-2.270.17911240.16382678X-RAY DIFFRACTION99.82
2.27-2.390.20281610.16932642X-RAY DIFFRACTION99.93
2.39-2.540.23211480.18412661X-RAY DIFFRACTION100
2.54-2.740.21131160.17932707X-RAY DIFFRACTION100
2.74-3.020.17931110.17612696X-RAY DIFFRACTION99.96
3.02-3.450.18261250.16952691X-RAY DIFFRACTION100
3.45-4.350.1611540.14772678X-RAY DIFFRACTION100
4.35-35.480.1771470.1632719X-RAY DIFFRACTION99.93
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)
10.313295070649-0.216332713296-0.03645640923610.1991125934940.05470498635780.2387222811660.2155032158980.4462528063290.475013038058-0.3838344777460.05217919092130.498742955991-0.237378954619-0.396126277701-0.0005299942703290.3822385607320.0158358752183-0.00656820005490.4289342706130.02507839558340.417219024358-32.452078936533.22400911289.44897013356
20.346567204387-0.464178165051-0.08266431091610.575519198771-0.05608095561290.2216860261710.023746063325-0.109249250341-0.07298169330530.01185001026680.2012521425910.07185701501110.4370724442220.05435115111580.006669238412550.354969505194-0.06434523841020.01758058576450.3370173876880.03503019283450.361332444587-32.891781767321.956521620421.1595015435
30.834651011544-0.645225366209-0.8248697460460.9894947186140.3267044646091.765048080980.00685113473923-0.192882152373-0.06799201434420.08833383481970.0448589803123-0.05837940919290.2702394182550.105422029472-2.92002671946E-50.297186715768-0.0267782438848-0.006519952462530.320659409712-0.005833491051290.310840239366-30.211996885727.945791268526.0553974831
40.104523536569-0.1441818555550.1244461529110.14089480733-0.1288050839820.1305072157750.4297275769650.431108736331-0.108110539818-0.188052560263-0.3616358243720.0416714097284-0.0500741594102-0.655552062914-0.0005084449298840.2849706530260.03660026299820.03036849789350.5170054057360.01054417279840.340183353518-44.11521063737.82260995422.1398219746
50.126864283888-0.1134907415960.07871970035980.0636227672356-0.08608189304790.112516620006-0.182814080145-0.1522066366670.5503736508250.2212577938520.124148776266-0.0695389131154-0.2436970467510.06203498254928.62871599292E-50.332332053652-0.02940417421380.01212124875910.410447979285-0.02876913432060.383065054488-38.271319841337.91448160332.3733503214
60.01392994631750.001765059973080.0456776575250.1399702855290.1172873382790.4878433135170.3694698787780.1691922796240.841844459074-0.3922167284710.122254738487-0.449402607453-0.666793075591-0.4025036903550.001325961045060.4665481735780.05813909017730.1018512713040.4336188305590.1049494170970.527648051062-44.961345891648.268127326527.2988817319
70.176727319030.126706934157-0.1626287411830.3472998723950.08899744043480.352273915290.285908480663-0.1705697650860.4810410829810.305592959173-0.0869375920020.0883052999555-0.4468588956110.194153669631-0.000333267662080.41900130359-0.06971616243250.04287184043210.333925647025-0.03069943651320.398183652894-23.335884646339.961918319916.5271875754
80.6618226840750.111733090975-0.4998481301160.695094488976-0.3673607638580.495569043306-0.0886958431896-0.0244873337301-0.0874738526411-0.101448776521-0.00558936576709-0.1817285989010.2440131777540.352609631592-0.0004143076758950.280601765124-0.01357013251840.00601063225170.404331922964-0.004697667135990.337895602481-16.744184480427.5966217329.09743446222
90.07886927910390.0178214488102-0.04825229404930.1168964861320.2800643482320.685543445717-0.168353970857-0.0468579353525-0.308576842391-0.144404108795-0.0472488611864-0.3149468100920.7885562366840.3276326217312.38355092579E-50.4713184661810.04318697562430.04609081719620.3802092204540.04737967178650.411335854821-16.436384043121.22290322028.05977854424
100.07420292024660.09358844793640.07019860271490.2140149187620.1273490685870.3448935343090.1502858211610.1454229510440.1702351466470.206450579818-0.045942018136-0.0825555342831-0.423983689380.2280002425210.0002082654875620.329610408405-0.05422394787640.02203780347010.4012774826390.004794742727180.351242688845-14.783631893740.35638775742.60349104514
110.005189644446090.00655789795489-0.05107472557580.1917316883230.02496320245490.143840640497-0.112525620840.420310410935-0.27924383769-0.481405564418-0.0695783510881-0.1073264844520.2675079843150.2218148182660.0004629207899010.344139042084-0.04947530257770.01331470453160.411747176212-0.005663525184610.317677975438-16.56400446334.5577352066-6.10506586171
12-0.00566250192652-0.0124433360622-0.0280400271070.1174332781140.2275418889220.4120180249910.1161342331170.2531940167840.08994336947140.02648357879340.2343282261410.24926257535-0.695585928602-0.6822480815150.0006445467746330.4115862477510.03479296030350.04267749031350.4436847071680.05026440295740.362469047479-21.417101865445.1013004983-7.96742302083
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 19 )AA4 - 191 - 16
22chain 'A' and (resid 20 through 32 )AA20 - 3217 - 29
33chain 'A' and (resid 33 through 83 )AA33 - 8330 - 80
44chain 'A' and (resid 84 through 94 )AA84 - 9481 - 91
55chain 'A' and (resid 95 through 107 )AA95 - 10792 - 104
66chain 'A' and (resid 108 through 125 )AA108 - 125105 - 122
77chain 'B' and (resid 4 through 19 )BB4 - 191 - 16
88chain 'B' and (resid 20 through 54 )BB20 - 5417 - 51
99chain 'B' and (resid 55 through 72 )BB55 - 7252 - 69
1010chain 'B' and (resid 73 through 94 )BB73 - 9470 - 91
1111chain 'B' and (resid 95 through 107 )BB95 - 10792 - 104
1212chain 'B' and (resid 108 through 123 )BB108 - 123105 - 120

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