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- PDB-6ivl: Crystal structure of a membrane protein L259A -

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Basic information

Entry
Database: PDB / ID: 6ivl
TitleCrystal structure of a membrane protein L259A
ComponentsIbestrophin
KeywordsMEMBRANE PROTEIN
Function / homologyUPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / plasma membrane / ACETIC ACID / Ibestrophin / Ibestrophin
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKittredge, A. / Fukuda, F. / Zhang, Y. / Yang, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
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 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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.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.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

Downloads & links

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Assembly

Deposited unit
A: Ibestrophin
B: Ibestrophin
C: Ibestrophin
D: Ibestrophin
E: Ibestrophin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,26528
Polymers168,9465
Non-polymers1,31923
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28080 Å2
ΔGint-822 kcal/mol
Surface area48050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.350, 160.539, 161.878
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
Ibestrophin / Predicted membrane protein / YneE protein


Mass: 33789.164 Da / Num. of mol.: 5 / Mutation: L259A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U30_16350, B4U35_20780, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, D0897_06110, DXF97_13395, DY552_11160, DZB15_ ...Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U30_16350, B4U35_20780, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, D0897_06110, DXF97_13395, DY552_11160, DZB15_11820, NCTC11679_02573, NCTC13465_00112, NCTC5052_01714, NCTC8849_03195, NCTC9637_03467, NCTC9645_05950, NCTC9661_03571, SAMEA104305404_11875, SAMEA23986918_00256, SAMEA24002668_02597, SAMEA3649709_04169, SAMEA4394730_00268
Production host: Escherichia coli (E. coli) / References: UniProt: W9BH30, UniProt: W1ELP7*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.4 Å3/Da / Density % sol: 72.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.05 M zinc acetate, 6% v/v ethylene glycol, 0.1 M 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-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.4→161.9 Å / Num. obs: 41709 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Net I/σ(I): 15.4
Reflection shellResolution: 3.4→3.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4641 / CC1/2: 0.757 / Rpim(I) all: 0.345 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.8 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24359 2088 5 %RANDOM
Rwork0.20861 ---
obs0.21039 39546 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 103.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20 Å2
2--0.11 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 3.4→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10699 0 26 10 10735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01210938
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.62614891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32951340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82720.712562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.076151848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.061590
X-RAY DIFFRACTIONr_chiral_restr0.0730.21470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028226
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.17510.1985376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.8915.2816710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.79910.5685562
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.76417661
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 150 -
Rwork0.264 2861 -
obs--100 %

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