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- PDB-5zd4: Crystal structure of MBP-fused BIL1/BZR1 in complex with double-s... -

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Basic information

Entry
Database: PDB / ID: 5zd4
TitleCrystal structure of MBP-fused BIL1/BZR1 in complex with double-stranded DNA
Components
  • DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
  • Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1
KeywordsTRANSCRIPTION / Transcription factor / Brassinosteroid / Plant
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 / outer membrane-bounded 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 / outer membrane-bounded 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
Similarity search - Domain/homology
alpha-maltose / DNA / DNA (> 10) / Maltose/maltodextrin-binding periplasmic protein / Protein BRASSINAZOLE-RESISTANT 1
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Arabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsNosaki, S. / Miyakawa, T. / Xu, Y. / Nakamura, A. / Hirabayashi, K. / Tanokura, M.
CitationJournal: Nat Plants / Year: 2018
Title: Structural basis for brassinosteroid response by BIL1/BZR1.
Authors: Nosaki, S. / Miyakawa, T. / Xu, Y. / Nakamura, A. / Hirabayashi, K. / Asami, T. / Nakano, T. / Tanokura, M.
History
DepositionFeb 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)219,45319
Polymers217,6508
Non-polymers1,80411
Water5,098283
1
C: Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6969
Polymers108,8254
Non-polymers8715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-18 kcal/mol
Surface area40230 Å2
MethodPISA
2
A: Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,75810
Polymers108,8254
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-19 kcal/mol
Surface area41360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.701, 92.603, 111.967
Angle α, β, γ (deg.)90.00, 100.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Maltose-binding periplasmic protein,Protein BRASSINAZOLE-RESISTANT 1 / MBP / MMBP / Maltodextrin-binding protein / Protein BIN2 SUBSTRATE 2


Mass: 49819.445 Da / Num. of mol.: 4 / Mutation: D108A,K109A,E198A,N199A,K265A,E385A,K388A,D389A
Source method: isolated from a genetically manipulated source
Details: Chimera protein of residues 27-392 from Maltose-binding periplasmic protein (UNP P0AEY0), and residues 21-104 from Protein BRASSINAZOLE-RESISTANT 1 (UNP Q8S307)
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: malE, Z5632, ECs5017, BZR1, BIS2, At1g75080, F9E10_7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEY0, UniProt: Q8S307
#2: DNA chain
DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')


Mass: 4593.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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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: 51.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50mM sodium cacodylate (pH 6.5), 200mM potassium chloride, 10% (w/v) polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→47.33 Å / Num. obs: 109100 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 21.2
Reflection shellResolution: 2.17→2.21 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5420 / CC1/2: 0.897 / Rpim(I) all: 0.32 / Rrim(I) all: 0.578 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQZ

5iqz


Resolution: 2.17→43.598 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 5449 5 %
Rwork0.2166 --
obs0.218 109005 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→43.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13381 1220 120 283 15004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615178
X-RAY DIFFRACTIONf_angle_d0.78620840
X-RAY DIFFRACTIONf_dihedral_angle_d21.7735668
X-RAY DIFFRACTIONf_chiral_restr0.0532272
X-RAY DIFFRACTIONf_plane_restr0.0042489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.19470.31791810.27383479X-RAY DIFFRACTION100
2.1947-2.22050.33581760.27143410X-RAY DIFFRACTION100
2.2205-2.24760.29641950.27043430X-RAY DIFFRACTION100
2.2476-2.2760.30621920.27233444X-RAY DIFFRACTION100
2.276-2.3060.30851770.26113468X-RAY DIFFRACTION100
2.306-2.33750.29111760.25993419X-RAY DIFFRACTION100
2.3375-2.37090.28711960.25233445X-RAY DIFFRACTION100
2.3709-2.40630.28721830.24973404X-RAY DIFFRACTION100
2.4063-2.44390.26061810.24793442X-RAY DIFFRACTION100
2.4439-2.4840.30521910.25533423X-RAY DIFFRACTION100
2.484-2.52680.26431930.25373430X-RAY DIFFRACTION100
2.5268-2.57280.2711740.2463461X-RAY DIFFRACTION100
2.5728-2.62220.27061770.24393453X-RAY DIFFRACTION100
2.6222-2.67570.27871900.24333448X-RAY DIFFRACTION100
2.6757-2.73390.2951900.25413424X-RAY DIFFRACTION100
2.7339-2.79750.281770.26333483X-RAY DIFFRACTION100
2.7975-2.86750.251850.25393443X-RAY DIFFRACTION100
2.8675-2.9450.28131900.25433439X-RAY DIFFRACTION100
2.945-3.03160.2821830.25093453X-RAY DIFFRACTION100
3.0316-3.12940.27881860.2563451X-RAY DIFFRACTION100
3.1294-3.24120.26571910.24453394X-RAY DIFFRACTION100
3.2412-3.3710.23751860.23293479X-RAY DIFFRACTION100
3.371-3.52430.2571820.21493472X-RAY DIFFRACTION100
3.5243-3.710.26791480.21133495X-RAY DIFFRACTION100
3.71-3.94230.22481810.19783460X-RAY DIFFRACTION100
3.9423-4.24650.18471820.17753453X-RAY DIFFRACTION100
4.2465-4.67340.18411940.16223458X-RAY DIFFRACTION99
4.6734-5.34860.19691590.16723511X-RAY DIFFRACTION100
5.3486-6.73470.21871630.19463484X-RAY DIFFRACTION99
6.7347-43.60710.19391700.17213501X-RAY DIFFRACTION97
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)
14.5591-0.6555-1.98653.08030.66713.08870.1401-0.40020.27420.06640.0312-0.0238-0.23640.2627-0.14550.3202-0.0650.0490.25450.020.2385-2.617614.364311.4523
23.9269-1.05990.23014.0347-0.79962.93720.041-0.4054-0.67430.42330.0673-0.12950.8384-0.1113-0.08570.5059-0.0759-0.08520.24610.02130.3794-6.3398-36.791827.7404
30.86950.0540.09341.5490.24020.929-0.4398-0.19180.13240.46820.7325-0.791-0.04280.6629-0.3180.69470.1838-0.17481.2416-0.65980.90183.716911.382945.5556
41.80650.8438-0.21483.46690.00042.7362-0.1007-0.05380.06650.50040.40780.1572-0.36670.0255-0.29590.46210.16660.06530.4882-0.03190.2356-21.177715.541942.6999
51.369-0.16220.10371.5335-1.07070.978-0.08680.16180.03730.92790.4393-0.8162-0.44470.6568-0.33660.72120.071-0.19081.1207-0.54880.7436-1.089920.610749.9723
61.26930.1349-0.09392.5139-0.41441.5322-0.3373-0.1783-0.11620.52470.6039-0.4115-0.01260.1818-0.24740.46350.1983-0.02330.5881-0.12870.3432-14.89313.295746.1291
73.33810.7878-0.01266.81794.71236.60860.1226-0.1723-0.18460.20340.2224-0.36310.74130.1403-0.35160.29610.016-0.07640.18290.02120.25373.9003-28.829831.8719
84.21620.8782-0.83813.9736-1.53441.974-0.08790.4268-1.1556-0.4190.08720.1841.3115-0.4303-0.01230.9183-0.1634-0.11670.3437-0.04190.6096-7.8001-43.944519.6311
91.5322-0.08841.10343.1246-1.92234.85870.2755-0.2755-0.06280.56320.0990.08580.5354-0.5944-0.34150.3144-0.122-0.03970.30850.01630.2544-5.965-23.82528.6696
102.18850.0773-0.42453.64031.32939.86230.2165-0.1973-0.13210.1210.1525-0.33260.20840.4002-0.34740.2452-0.0442-0.04640.2067-0.01280.2484-2.9254-23.76524.8273
113.65710.3264-0.87411.0047-0.32811.5620.1229-0.39170.010.0989-0.138-0.098-0.00720.54610.01530.27180.0082-0.02410.4239-0.00720.141639.7605-13.315243.8613
120.5568-0.4854-0.00853.7122-2.54191.9539-0.1162-0.00040.0866-0.30140.2460.23530.0208-0.646-0.16890.6703-0.0962-0.06650.7578-0.09920.391745.700929.473230.0119
133.8518-0.3114-0.52511.3747-0.24582.0912-0.01820.16080.0643-0.03490.06580.1193-0.0081-0.4395-0.03730.2271-0.0152-0.01830.23110.00750.147553.2029-15.182110.9428
140.62150.99010.26945.91573.01381.6614-0.0388-0.09-0.03460.68680.3137-0.33670.03120.5846-0.24850.75290.1222-0.10850.76760.11080.473346.814328.886225.5576
150.0858-0.2416-0.71640.70152.13047.11250.0297-0.4368-0.07840.28480.17440.1151.41310.1134-0.19990.70340.0759-0.03640.82540.04710.347546.800423.56129.9336
160.13850.1741-1.10290.2249-1.4559.31990.0564-0.4001-0.18120.02820.2898-0.00931.7130.0708-0.33220.73660.0476-0.07420.83590.05740.36645.270623.523525.6985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid -367 through 26 )
2X-RAY DIFFRACTION2chain 'C' and (resid 27 through 88 )
3X-RAY DIFFRACTION3chain 'D' and (resid -360 through -263 )
4X-RAY DIFFRACTION4chain 'D' and (resid -262 through -123 )
5X-RAY DIFFRACTION5chain 'D' and (resid -122 through -54 )
6X-RAY DIFFRACTION6chain 'D' and (resid -53 through 26 )
7X-RAY DIFFRACTION7chain 'D' and (resid 27 through 54 )
8X-RAY DIFFRACTION8chain 'D' and (resid 55 through 88 )
9X-RAY DIFFRACTION9chain 'G' and (resid -3 through 11 )
10X-RAY DIFFRACTION10chain 'H' and (resid -3 through 11 )
11X-RAY DIFFRACTION11chain 'A' and (resid -367 through -17 )
12X-RAY DIFFRACTION12chain 'A' and (resid -16 through 88 )
13X-RAY DIFFRACTION13chain 'B' and (resid -366 through -17 )
14X-RAY DIFFRACTION14chain 'B' and (resid -16 through 88 )
15X-RAY DIFFRACTION15chain 'E' and (resid -3 through 11 )
16X-RAY DIFFRACTION16chain 'F' and (resid -3 through 11 )

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