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- PDB-7vn5: Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vn5
TitleCrystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning TTCACGTGAA
Components
  • DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
  • Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
KeywordsTRANSCRIPTION / Transcription factor-DNA complex
Function / homology
Function and homology information


plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / DNA-binding transcription factor activity ...plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / nucleus / cytosol
Similarity search - Function
BZR family / BES1/BZR1 plant transcription factor, N-terminal / BES1/BZR1 plant transcription factor, N-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
alpha-maltose / DNA / DNA (> 10) / Maltodextrin-binding protein / Protein BRASSINAZOLE-RESISTANT 1
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
Arabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNosaki, S. / Tanokura, M. / Miyakawa, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05835, 19H04855, 19K23658, 21H02114 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101077 Japan
CitationJournal: Nat.Plants / Year: 2022
Title: Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout.
Authors: Nosaki, S. / Mitsuda, N. / Sakamoto, S. / Kusubayashi, K. / Yamagami, A. / Xu, Y. / Bui, T.B.C. / Terada, T. / Miura, K. / Nakano, T. / Tanokura, M. / Miyakawa, T.
History
DepositionOct 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,22425
Polymers212,0478
Non-polymers2,17617
Water7,404411
1
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,20514
Polymers106,0244
Non-polymers1,18110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-1 kcal/mol
Surface area40760 Å2
MethodPISA
2
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,01911
Polymers106,0244
Non-polymers9957
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-13 kcal/mol
Surface area41500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.622, 93.923, 112.750
Angle α, β, γ (deg.)90.000, 100.646, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 / Protein BIN2 SUBSTRATE 2


Mass: 48419.836 Da / Num. of mol.: 4 / Mutation: D82A,K83A,E172A,N173A,K239A,E359A,K362A,D363A
Source method: isolated from a genetically manipulated source
Details: The fused Maltose binding protein is derived from Escherichia coli O157:H7
Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) Arabidopsis thaliana (thale cress)
Strain: FS14 / Gene: malE, JW3994, BZR1, BIS2, At1g75080, F9E10_7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P1LXE0, UniProt: Q8S307
#2: DNA chain
DNA (5'-D(*TP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 4592.022 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM sodium cacodylate pH 6.5, 200 mM ammonium acetate and 10 mM calcium chloride and 10%

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.96 Å / Num. obs: 152246 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 3.4
Reflection shellResolution: 1.95→1.98 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 152246 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZD4
Resolution: 1.95→35.82 Å / SU ML: 0.2425 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3741
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2439 7634 5.02 %
Rwork0.2091 144384 -
obs0.2108 152018 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13592 1220 144 411 15367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007315411
X-RAY DIFFRACTIONf_angle_d0.835121142
X-RAY DIFFRACTIONf_chiral_restr0.05552306
X-RAY DIFFRACTIONf_plane_restr0.00512526
X-RAY DIFFRACTIONf_dihedral_angle_d23.28335761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.352560.34844X-RAY DIFFRACTION99.94
1.97-20.35252600.27954788X-RAY DIFFRACTION99.88
2-2.020.28932560.27684836X-RAY DIFFRACTION99.82
2.02-2.050.31382520.26284803X-RAY DIFFRACTION99.86
2.05-2.070.29282810.25224786X-RAY DIFFRACTION99.88
2.07-2.10.27912500.25174851X-RAY DIFFRACTION99.86
2.1-2.130.3072760.24474803X-RAY DIFFRACTION99.86
2.13-2.160.28882650.2514797X-RAY DIFFRACTION99.78
2.16-2.20.27272460.22854841X-RAY DIFFRACTION99.76
2.2-2.230.2592290.23594849X-RAY DIFFRACTION99.8
2.23-2.270.30112610.23144779X-RAY DIFFRACTION99.86
2.27-2.310.24362960.22554769X-RAY DIFFRACTION99.69
2.31-2.360.28442610.22154877X-RAY DIFFRACTION99.81
2.36-2.40.26112610.22714826X-RAY DIFFRACTION99.71
2.4-2.460.28612360.23454810X-RAY DIFFRACTION99.66
2.46-2.510.25222690.22924803X-RAY DIFFRACTION99.69
2.51-2.580.29452530.22724844X-RAY DIFFRACTION99.53
2.58-2.650.25042380.21664802X-RAY DIFFRACTION99.45
2.65-2.720.26022470.21824857X-RAY DIFFRACTION99.59
2.72-2.810.26112450.22774817X-RAY DIFFRACTION99.7
2.81-2.910.28572510.2374833X-RAY DIFFRACTION99.61
2.91-3.030.26322570.23244845X-RAY DIFFRACTION99.11
3.03-3.170.27982580.22994752X-RAY DIFFRACTION98.84
3.17-3.330.25572670.22254794X-RAY DIFFRACTION98.69
3.33-3.540.23962650.21744779X-RAY DIFFRACTION98.52
3.54-3.820.2252510.19954804X-RAY DIFFRACTION98.83
3.82-4.20.21642380.17994842X-RAY DIFFRACTION98.76
4.2-4.810.16152260.16094815X-RAY DIFFRACTION98.32
4.81-6.050.21432550.17254789X-RAY DIFFRACTION97.28
6.05-35.820.17812280.1624749X-RAY DIFFRACTION94.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.01711800809950.06383831781740.1773867076960.510611434711.418669666624.018972757460.686125705317-0.0279920757585-0.2036700606060.196697331624-0.0826364360983-0.1152164893581.117639568160.0614496302119-0.610179223091.085267802160.0602778200949-0.1456913073951.318391781640.04745492459920.58509750325746.73458129823.523375381629.9197207234
20.0293757916492-0.02570571789740.1644985703010.061494877769-0.3761761875632.010272977780.4838734780560.138356469615-0.175941628448-0.14155258022-0.1879498608270.1807299021061.22646463150.161207526152-0.2769313922691.113934842350.0945778577133-0.1048821076611.32571021981-0.03447035017170.59547985500645.250348600923.446584868625.6014161782
37.84437839373-0.1152610001270.6604989981324.907073200690.5188786120224.580651399820.185443658933-0.6572253635580.08309859115670.4111304113830.09655278035690.848666802583-0.331325488637-0.705357818436-0.2554107397470.3316257363540.05944310491510.1258319856870.3618195379560.08690694134330.306442274742-21.007351678818.248941761618.8463126668
45.514642303071.41175089964-0.2359729710883.14367433503-0.1144140205682.824606342730.09073241074810.0981718115899-0.29134475855-0.1575478531140.05334991415150.3148640528630.0883353504819-0.291517122118-0.1410632745740.2100771920620.0368176680564-0.004564703857160.1721884685720.01091060151410.206316818924-13.102492571110.80290939986.57494079618
52.84975535977-0.203036436105-0.3469140393663.74369123360.9185540390322.405065545030.0741054282464-0.1834559982230.228510603149-0.07096563197560.0379163352052-0.429862184612-0.3092875840650.527543493906-0.1101665195070.247998051387-0.07399796340560.04831029463720.3070727665260.03224587313250.21627065666111.033292253215.510658456713.767331488
64.497409493520.118224418578-0.7268414981862.23661733083-0.2188508587262.227981241950.2291111610240.1651813532160.445634339803-0.1456426748270.02830654094740.283774508901-0.464140582655-0.249375315578-0.2543958348660.3194146258780.037224846470.02149670125270.2052463834290.05531118479180.181559207828-10.480349436120.73042978986.53333188545
72.95749829757-0.6388684385540.4382002484822.268899958871.129298867941.860694084860.09649789494-0.311883485083-0.353227095624-0.121576253598-0.0742410095364-0.03110475884660.3039005620550.208120563795-0.02280083283220.205266707653-0.003650573991670.07084060437150.2450291796830.05629546799440.2106724214973.729562853553.738474349529.77543334058
83.16891542361-2.721411168981.663468757458.55234420144-7.869775351139.734617468180.114396266672-0.0968809188634-0.104216857563-0.4016964139550.1550834321510.1377265213090.659596424409-0.226422305379-0.2309123344430.204168009743-0.0370159979975-0.0153307174270.159282157376-0.01405023318470.147899183144-13.2287485394-29.58109672922.2079892394
93.74974557435-1.382307359620.10555378486.046369562032.171578122931.31832135292-0.127441854368-0.667350155729-0.8460577386160.6332515934520.203030964964-0.1969875816921.106788460390.274201720533-0.069855870740.826642181820.116152548417-0.03500263232190.3031255551640.1211482646080.467721297025-1.49060843884-44.424292733734.7233951452
103.400591593520.7701278103510.04468139270161.33464570762-0.1290449431491.866038997650.03181583028710.1779549883430.02344457702950.1023518267270.0783368421895-0.00862283862438-0.117369794285-0.19967963843-0.1021689068750.2764839118630.05125424352810.01108438702040.226521311624-0.003310641071530.151402295181-8.0217500945814.034101358144.5553907523
112.59640238041.262559664970.6071981630063.323814368490.9520745127762.943559011160.1052642146320.0658573608687-0.3398019517-0.109674902870.114538240496-0.1317141562080.8369907757630.0317936345711-0.1993409062530.4297383630360.0307741176619-0.02855074105440.1904060392010.05426407001170.253193139887-2.62948310247-37.287485067726.5441473855
120.0707486288492-0.0436255634141-0.7956092561070.2669301609220.09758297456212.041913120080.111920753611-0.0746090357922-0.01950639532270.1291416977290.06392289772810.009457895153420.270956658912-0.577622828719-0.26205969260.35409698275-0.0160912041386-0.01175544373180.3089002299230.01906013672050.220651328761-6.62972926655-24.398230814229.5225613692
131.0581200131-0.393046839895-2.329774158221.908331176092.648112674098.804754376050.143342314533-0.3243704985220.02361365330460.03382732687150.224891543305-0.1422824851430.08213669673060.830281210886-0.3560460160320.23865588462-0.0202765120857-0.03911034326580.229356951094-0.02129367205390.202972377432-3.32342422242-24.426868005925.677095624
145.40537685526-0.105608132657-0.1290917482790.8961105440920.01587846176190.7659456708110.1338864185690.3219640001570.291263572105-0.0439819366501-0.1550210814320.0225899338506-0.06649482997930.1489894100160.02432879058680.2486755896390.06336736815850.01904251840770.2850873570530.0370703816310.17533701166739.6992595608-13.922833047144.2445398144
152.02067765451-1.067496234920.6895054550922.64938613478-2.932807393513.39910162366-0.08863104651510.496737178799-0.1422150945450.109816798410.3509904665180.227525405441-0.624256573613-0.49274338989-0.265939257980.7511532161660.01654803396880.003744337443380.721089668586-0.1197580533240.48908730772945.482740352329.124537788529.8262637893
163.4851400263-0.00275758706859-0.5303573463241.21549916601-0.1855751845312.338516602910.02559521111250.1616704846590.0729052328852-0.07825571318480.004459851015850.2034801035770.155049814577-0.937153531329-0.02831208150660.21617210482-0.0995876479014-0.01343926210030.5955955626690.008128795608690.20833044024453.0325644846-15.490922882811.3599570409
171.318620600481.186732660330.5966427449821.09580411750.4585873193271.44284976080.0559486590724-0.288199150699-0.2233112924920.5092622426990.0879628658207-0.252202824076-0.3688351954260.302897703253-0.1214576247680.8537070866730.1341362216250.01807875539591.006039797640.1987264140030.59877369210946.588934458728.496144299125.7431109288
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid -3 through 11 )EK-3 - 11
22chain 'F' and (resid -3 through 11 )FL-3 - 11
33chain 'C' and (resid -348 through -306 )CA-348 - -3061 - 43
44chain 'C' and (resid -305 through -230 )CA-305 - -23044 - 119
55chain 'C' and (resid -229 through -103 )CA-229 - -103120 - 246
66chain 'C' and (resid -102 through -34 )CA-102 - -34247 - 315
77chain 'C' and (resid -33 through 26 )CA-33 - 26316 - 375
88chain 'C' and (resid 27 through 54 )CA27 - 54376 - 403
99chain 'C' and (resid 55 through 88 )CA55 - 88404 - 437
1010chain 'D' and (resid -348 through 26 )DC-348 - 261 - 375
1111chain 'D' and (resid 27 through 88 )DC27 - 88376 - 437
1212chain 'G' and (resid -3 through 11 )GE-3 - 11
1313chain 'H' and (resid -3 through 11 )HF-3 - 11
1414chain 'A' and (resid -347 through 4 )AG-347 - 41 - 352
1515chain 'A' and (resid 5 through 88 )AG5 - 88353 - 436
1616chain 'B' and (resid -347 through 3 )BI-347 - 31 - 351
1717chain 'B' and (resid 4 through 88 )BI4 - 88352 - 436

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