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- PDB-5l25: Crystal Structure of Arabidopsis thaliana Bor1 -

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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 / solute:inorganic anion antiporter activity / monoatomic anion transport / vacuolar membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 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

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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

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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 %

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