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- PDB-6iv3: Crystal structure of a bacterial Bestrophin homolog from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 6iv3
TitleCrystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a mutation W252A
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: 2.515 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.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)169,12620
Polymers168,1455
Non-polymers98115
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25620 Å2
ΔGint-668 kcal/mol
Surface area48470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.461, 159.607, 162.674
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: 33629.031 Da / Num. of mol.: 5 / Mutation: W252A
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.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 4.38 Å3/Da / Density % sol: 71.92 %
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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.52→66.11 Å / Num. obs: 99774 / % possible obs: 98.7 % / Redundancy: 3.4 % / Net I/σ(I): 12.75
Reflection shellResolution: 2.52→2.61 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.515→66.106 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 2006 2.02 %
Rwork0.2335 --
obs0.2341 99439 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.515→66.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10672 0 0 80 10752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110918
X-RAY DIFFRACTIONf_angle_d1.05514869
X-RAY DIFFRACTIONf_dihedral_angle_d10.2216538
X-RAY DIFFRACTIONf_chiral_restr0.0511778
X-RAY DIFFRACTIONf_plane_restr0.0071870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5148-2.57770.38161410.31776549X-RAY DIFFRACTION94
2.5777-2.64740.29121440.30046930X-RAY DIFFRACTION99
2.6474-2.72530.33021370.27946874X-RAY DIFFRACTION99
2.7253-2.81330.311430.26746946X-RAY DIFFRACTION100
2.8133-2.91380.29531430.25926996X-RAY DIFFRACTION100
2.9138-3.03050.31981430.25886996X-RAY DIFFRACTION100
3.0305-3.16840.26611420.25076991X-RAY DIFFRACTION100
3.1684-3.33540.27691390.24146983X-RAY DIFFRACTION100
3.3354-3.54440.27691470.23116993X-RAY DIFFRACTION99
3.5444-3.81810.22561420.21456962X-RAY DIFFRACTION99
3.8181-4.20220.2521410.2036934X-RAY DIFFRACTION98
4.2022-4.81010.22881450.18987062X-RAY DIFFRACTION100
4.8101-6.05960.24631440.25557102X-RAY DIFFRACTION99
6.0596-66.12850.27591550.23767115X-RAY DIFFRACTION96

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