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

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Basic information

Entry
Database: PDB / ID: 6jlf
TitleCrystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae D179A mutation - HR
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: 2.548 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
DepositionMar 5, 2019Deposition 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.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: Bestrophin homolog
B: Bestrophin homolog
C: Bestrophin homolog
D: Bestrophin homolog
E: Bestrophin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,65616
Polymers168,9365
Non-polymers71911
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25420 Å2
ΔGint-601 kcal/mol
Surface area46900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.970, 159.468, 161.901
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: 33787.230 Da / Num. of mol.: 5 / Mutation: D179A
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.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05M ZnAce, 6.6% PEG 8000, 0.1M Na-Cacodylat (pH 6.0), 6% EG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.548→93.195 Å / Num. obs: 95113 / % possible obs: 98.2 % / Redundancy: 3.4 % / Net I/σ(I): 18.74
Reflection shellResolution: 2.548→2.64 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.548→93.195 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.22
RfactorNum. reflection% reflection
Rfree0.2759 1998 2.1 %
Rwork0.2297 --
obs0.2307 95092 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.548→93.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10477 0 11 53 10541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110709
X-RAY DIFFRACTIONf_angle_d1.21314598
X-RAY DIFFRACTIONf_dihedral_angle_d8.8966372
X-RAY DIFFRACTIONf_chiral_restr0.0591752
X-RAY DIFFRACTIONf_plane_restr0.0081824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5481-2.61180.36161370.32466500X-RAY DIFFRACTION97
2.6118-2.68250.37641380.30576602X-RAY DIFFRACTION99
2.6825-2.76140.32941450.29726623X-RAY DIFFRACTION99
2.7614-2.85050.34241430.29016585X-RAY DIFFRACTION98
2.8505-2.95240.29421380.276516X-RAY DIFFRACTION97
2.9524-3.07060.27641430.24896683X-RAY DIFFRACTION100
3.0706-3.21040.29741460.25756675X-RAY DIFFRACTION99
3.2104-3.37970.29581490.25036699X-RAY DIFFRACTION99
3.3797-3.59140.31711380.23966647X-RAY DIFFRACTION99
3.5914-3.86870.26631410.21716545X-RAY DIFFRACTION97
3.8687-4.2580.27061440.20656735X-RAY DIFFRACTION99
4.258-4.87420.21121460.19216760X-RAY DIFFRACTION99
4.8742-6.14080.27591420.24866655X-RAY DIFFRACTION97
6.1408-93.2570.27641480.21626869X-RAY DIFFRACTION96

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