[English] 日本語
Yorodumi
- PDB-5zd4: Crystal structure of MBP-fused BIL1/BZR1 in complex with double-s... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more