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- PDB-6iv1: Crystal structure of a bacterial Bestrophin homolog from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 6iv1
TitleCrystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a mutation I180T
ComponentsBestrophin homolog
KeywordsMEMBRANE PROTEIN / Bestrophin-1 / homolog / mutation / klebsiella pneumoniae
Function / homologyUPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / Ibestrophin
Function and homology information
Biological speciesKlebsiella pneumoniae IS53 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.18 Å
AuthorsKittredge, A. / Chen, S. / Yang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770801 China
CitationJournal: Commun Biol / Year: 2019
Title: Dual Ca2+-dependent gates in human Bestrophin1 underlie disease-causing mechanisms of gain-of-function mutations.
Authors: Ji, C. / Kittredge, A. / Hopiavuori, A. / Ward, N. / Chen, S. / Fukuda, Y. / Zhang, Y. / Yang, T.
History
DepositionDec 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bestrophin homolog
B: Bestrophin homolog
C: Bestrophin homolog
D: Bestrophin homolog
E: Bestrophin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,57619
Polymers168,6615
Non-polymers91614
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26030 Å2
ΔGint-659 kcal/mol
Surface area47420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.835, 159.247, 159.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Bestrophin homolog


Mass: 33732.109 Da / Num. of mol.: 5 / Mutation: I180T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae IS53 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1ELP7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M zinc acetate, 6% v/v ethylene glycol, 0.1M sodium cacodylate, pH 6.0, 6.6% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.18→112.84 Å / Num. obs: 42873 / % possible obs: 87.2 % / Redundancy: 1.9 % / Net I/σ(I): 8.18
Reflection shellResolution: 3.18→3.29 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3.18→112.84 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.888 / SU B: 26.109 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27567 2000 4.7 %RANDOM
Rwork0.24171 ---
obs0.24332 40862 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.485 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--3.66 Å20 Å2
3----3.57 Å2
Refinement stepCycle: 1 / Resolution: 3.18→112.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10570 0 14 8 10592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910800
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210551
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.97314717
X-RAY DIFFRACTIONr_angle_other_deg0.819324099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11851334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71422.654456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.825151799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.271589
X-RAY DIFFRACTIONr_chiral_restr0.0670.21755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022533
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_it8.4139.2685351
X-RAY DIFFRACTIONr_mcbond_other8.4049.2685350
X-RAY DIFFRACTIONr_mcangle_it12.93813.9246680
X-RAY DIFFRACTIONr_mcangle_other12.94213.9246681
X-RAY DIFFRACTIONr_scbond_it8.7449.8195449
X-RAY DIFFRACTIONr_scbond_other8.7439.8195450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.52314.5568038
X-RAY DIFFRACTIONr_long_range_B_refined19.47878.14413400
X-RAY DIFFRACTIONr_long_range_B_other19.47878.14713401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.18→3.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 143 -
Rwork0.423 2996 -
obs--87.53 %

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