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- PDB-6ivr: Crystal structure of a membrane protein W16A -

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Basic information

Entry
Database: PDB / ID: 6ivr
TitleCrystal structure of a membrane protein W16A
ComponentsIbestrophin
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


chloride channel activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel
Similarity search - Domain/homology
ACETIC ACID / Ibestrophin / Bestrophin family ion channel
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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.ptnr1_symmetry / _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

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)170,13434
Polymers168,5815
Non-polymers1,55329
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29420 Å2
ΔGint-819 kcal/mol
Surface area47800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.914, 159.568, 161.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Ibestrophin / Predicted membrane protein / YneE protein


Mass: 33716.109 Da / Num. of mol.: 5 / Mutation: W16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U27_02655, B4U30_16350, B4U35_20780, BB785_13310, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, CWQ24_13475, DM060_ ...Gene: yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U27_02655, B4U30_16350, B4U35_20780, BB785_13310, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, CWQ24_13475, DM060_34770, DM071_16710, DM078_14870, DM083_28480, DMR37_19630, DXF97_13395, NCTC11679_02573, NCTC13465_00112, NCTC5052_01714, NCTC8849_03195, NCTC9637_03467, NCTC9645_05950, NCTC9661_03571, SAMEA104305404_11875, SAMEA23986918_00256, SAMEA24002668_02597, SAMEA24012418_00268, SAMEA3649709_04169, SAMEA3673019_02937, SAMEA3727643_02313, SAMEA4394730_00268
Production host: Escherichia coli (E. coli) / References: UniProt: W9BH30, UniProt: W1ELP7*PLUS

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Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-ZN / ZINC ION / Predicted membrane protein / YneE protein


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 4.36 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: 2.8→161.7 Å / Num. obs: 73119 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.367 / Num. unique obs: 4443 / CC1/2: 0.524 / Rpim(I) all: 0.577 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.73 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.28 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24838 3668 5 %RANDOM
Rwork0.21738 ---
obs0.21899 69361 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2--0.04 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10726 0 38 63 10827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01210972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.62614935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32151341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07920.727564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36151857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0171590
X-RAY DIFFRACTIONr_chiral_restr0.0750.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028253
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_it3.7297.5365381
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.33111.2816715
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4377.8635591
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.10117607
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 238 -
Rwork0.314 5075 -
obs--99.92 %

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