[English] 日本語
Yorodumi
- PDB-5l25: Crystal Structure of Arabidopsis thaliana Bor1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l25
TitleCrystal Structure of Arabidopsis thaliana Bor1
ComponentsBoron transporter 1
KeywordsTRANSPORT PROTEIN / Membrane protein / SLC4 / anion exchanger
Function / homology
Function and homology information


borate transmembrane transport / response to boron-containing substance / cellular response to boron-containing substance levels / active borate transmembrane transporter activity / monoatomic ion homeostasis / solute:inorganic anion antiporter activity / monoatomic anion transport / vacuolar membrane / transmembrane transport / endosome membrane / plasma membrane
Similarity search - Function
Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.11 Å
AuthorsThurtle-Schmidt, B.H. / Stroud, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of Bor1 supports an elevator transport mechanism for SLC4 anion exchangers.
Authors: Thurtle-Schmidt, B.H. / Stroud, R.M.
History
DepositionJul 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Boron transporter 1


Theoretical massNumber of molelcules
Total (without water)73,2661
Polymers73,2661
Non-polymers00
Water00
1
A: Boron transporter 1

A: Boron transporter 1


Theoretical massNumber of molelcules
Total (without water)146,5312
Polymers146,5312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1530 Å2
ΔGint-16 kcal/mol
Surface area42520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.557, 184.557, 89.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Boron transporter 1


Mass: 73265.516 Da / Num. of mol.: 1 / Fragment: UNP residues 1-645
Source method: isolated from a genetically manipulated source
Details: The solvent content as calculated by Matthews coefficients is high since a significant portion of unit cell contains detergent. Additionally, the crystallized protein construct is 652 ...Details: The solvent content as calculated by Matthews coefficients is high since a significant portion of unit cell contains detergent. Additionally, the crystallized protein construct is 652 residues, of which the authors were able to model 399.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BOR1, At2g47160, T3D7.3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q8VYR7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium citrate pH 5.8, 300mM lithium sulfate, 10.5% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 4.1→20.07 Å / Num. obs: 11319 / % possible obs: 96.3 % / Redundancy: 12 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 19.3
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.631 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZF

4yzf


Resolution: 4.11→20.07 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.837 / Cross valid method: THROUGHOUT / ESU R Free: 0.84 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.39149 565 4.8 %RANDOM
Rwork0.35867 ---
obs0.3602 11319 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 257.892 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å2-0 Å20 Å2
2---4.74 Å2-0 Å2
3---9.48 Å2
Refinement stepCycle: LAST / Resolution: 4.11→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 0 0 2875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192937
X-RAY DIFFRACTIONr_bond_other_d00.022898
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9484009
X-RAY DIFFRACTIONr_angle_other_deg3.67736585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68822.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.686159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213307
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02676
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it32.12724.8721588
X-RAY DIFFRACTIONr_mcbond_other32.09524.8711587
X-RAY DIFFRACTIONr_mcangle_it49.81737.1621971
X-RAY DIFFRACTIONr_mcangle_other49.80537.1651972
X-RAY DIFFRACTIONr_scbond_it31.03426.9371348
X-RAY DIFFRACTIONr_scbond_other31.02326.941349
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other47.91939.592039
X-RAY DIFFRACTIONr_long_range_B_refined68.25512074
X-RAY DIFFRACTIONr_long_range_B_other68.25512073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.115→4.217 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 30 -
Rwork0.431 690 -
obs--83.43 %

+
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://pdbjlvh1.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