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- PDB-4wd8: Crystal structure of a bacterial Bestrophin homolog from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 4wd8
TitleCrystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae
ComponentsBestrophin domain protein
KeywordsMEMBRANE PROTEIN / Calcium-activated chloride channel / Macular degeneration / Single-wavelength anomalous diffraction (SAD) / Sodium channel / pentamer / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology:
Function and homology information
Biological speciesKlebsiella pneumoniae UHKPC96 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsYang, T. / Liu, Q. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107462 United States
CitationJournal: Science / Year: 2014
Title: Structure and selectivity in bestrophin ion channels.
Authors: Yang, T. / Liu, Q. / Kloss, B. / Bruni, R. / Kalathur, R.C. / Guo, Y. / Kloppmann, E. / Rost, B. / Colecraft, H.M. / Hendrickson, W.A.
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bestrophin domain protein
B: Bestrophin domain protein
C: Bestrophin domain protein
D: Bestrophin domain protein
E: Bestrophin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,13720
Polymers169,1565
Non-polymers98115
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26880 Å2
ΔGint-706 kcal/mol
Surface area48400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.079, 160.034, 161.881
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 domain protein


Mass: 33831.242 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae UHKPC96 (bacteria)
Gene: H215_4284 / Production host: Escherichia coli (E. coli) / References: UniProt: S7AS11
#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.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.84 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 131752 / % possible obs: 99.9 % / Redundancy: 12.4 % / Net I/σ(I): 11.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→38.961 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.93 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 12418 4.89 %
Rwork0.1962 --
obs0.1971 254129 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10636 0 15 365 11016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810924
X-RAY DIFFRACTIONf_angle_d0.95514806
X-RAY DIFFRACTIONf_dihedral_angle_d11.0763931
X-RAY DIFFRACTIONf_chiral_restr0.061761
X-RAY DIFFRACTIONf_plane_restr0.0051861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.33123570.30898176X-RAY DIFFRACTION100
2.3261-2.35350.2864100.30298037X-RAY DIFFRACTION100
2.3535-2.38220.30314060.28838137X-RAY DIFFRACTION100
2.3822-2.41230.3194010.29337998X-RAY DIFFRACTION100
2.4123-2.44410.32314500.28478075X-RAY DIFFRACTION100
2.4441-2.47760.29094760.27017972X-RAY DIFFRACTION100
2.4776-2.51290.29554250.25657997X-RAY DIFFRACTION100
2.5129-2.55050.28814250.24628044X-RAY DIFFRACTION100
2.5505-2.59030.25884610.24058093X-RAY DIFFRACTION100
2.5903-2.63280.24983610.23638104X-RAY DIFFRACTION100
2.6328-2.67810.23424140.22978058X-RAY DIFFRACTION100
2.6781-2.72680.23163140.21988133X-RAY DIFFRACTION100
2.7268-2.77930.22354490.20888054X-RAY DIFFRACTION100
2.7793-2.8360.24433890.20948082X-RAY DIFFRACTION100
2.836-2.89760.22463970.20068071X-RAY DIFFRACTION100
2.8976-2.9650.20174100.19918116X-RAY DIFFRACTION100
2.965-3.03910.21964430.19048003X-RAY DIFFRACTION100
3.0391-3.12130.19574010.18688075X-RAY DIFFRACTION100
3.1213-3.21310.23323940.19978073X-RAY DIFFRACTION100
3.2131-3.31670.21694150.19768064X-RAY DIFFRACTION100
3.3167-3.43520.21054410.18868040X-RAY DIFFRACTION100
3.4352-3.57260.19794540.17828062X-RAY DIFFRACTION100
3.5726-3.73510.19614410.1728010X-RAY DIFFRACTION100
3.7351-3.93190.17774040.16518095X-RAY DIFFRACTION100
3.9319-4.17790.20514010.16898051X-RAY DIFFRACTION100
4.1779-4.50010.16343910.16068055X-RAY DIFFRACTION100
4.5001-4.95220.19683960.16948127X-RAY DIFFRACTION100
4.9522-5.66690.21034160.19258051X-RAY DIFFRACTION100
5.6669-7.13250.26094890.22117983X-RAY DIFFRACTION100
7.1325-38.96670.16863870.1847875X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35531.0101-1.15240.8163-0.34464.677-0.3496-0.75050.21060.79970.3751-0.41770.54830.9198-0.10350.77060.3829-0.24270.7183-0.25420.4133-17.8184-14.608933.0096
22.5384-0.42251.23181.6105-0.38623.54510.021-0.0503-0.2945-0.04350.03180.15180.3535-0.086-0.03610.113-0.00070.00520.15640.00720.2598-14.1528-44.5482-2.5041
30.83730.58560.4823.17872.01762.5667-0.0318-0.35730.82670.06150.3077-1.0244-0.85360.5685-0.29650.63240.0057-0.26180.479-0.37550.7584-14.03382.570322.9661
42.2263-1.02330.12813.3370.70223.0906-0.03440.25550.442-0.28420.0921-0.9035-0.2250.5323-0.02150.152-0.03110.07560.29630.07310.4213-3.8248-24.0979-13.4518
53.7091-1.1152-2.58073.60930.78114.9913-0.2460.07970.21990.3852-0.27330.77050.0715-1.39890.40090.43850.2336-0.04680.6746-0.23890.5241-45.8873-2.470921.9135
62.5889-0.4114-0.45332.33450.60823.26490.05810.25460.2896-0.2984-0.01060.2405-0.303-0.2356-0.040.2059-0.029-0.03670.20890.08570.2207-43.6094-22.3347-19.9198
72.0572-0.8327-0.69744.91381.42441.8777-0.03650.03970.7317-0.4219-0.0635-0.0585-1.2421-0.60210.0620.77170.2051-0.12480.3501-0.14110.547-31.33099.772615.8191
82.3453-0.4806-0.29273.37350.47552.8289-0.03720.40350.321-0.5184-0.0832-0.2917-0.61540.110.08930.3484-0.0306-0.01560.35270.17190.2775-21.6287-11.1403-24.4761
93.43070.8724-0.74711.3710.89325.4967-0.1917-0.632-0.04591.07270.04370.25540.8475-0.22970.12650.73560.13510.03260.4447-0.09010.3264-37.3795-17.490132.8362
103.59520.0802-0.21442.18870.15332.6815-0.0573-0.0951-0.31760.0676-0.01320.1450.2793-0.13150.05920.1254-0.0275-0.02150.14980.01060.248-39.482-42.7694-6.2059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 22:74 or resseq 206:260)
2X-RAY DIFFRACTION2chain A and (resseq 75:205 or resseq 261:289)
3X-RAY DIFFRACTION3chain B and (resseq 22:74 or resseq 206:260)
4X-RAY DIFFRACTION4chain B and (resseq 75:205 or resseq 261:285)
5X-RAY DIFFRACTION5chain C and (resseq 22:74 or resseq 206:260)
6X-RAY DIFFRACTION6chain C and (resseq 75:205 or resseq 261:291)
7X-RAY DIFFRACTION7chain D and (resseq 22:74 or resseq 206:260)
8X-RAY DIFFRACTION8chain D and (resseq 75:205 or resseq 261:289)
9X-RAY DIFFRACTION9chain E and (resseq 24:74 or resseq 206:260)
10X-RAY DIFFRACTION10chain E and (resseq 75:205 or resseq 261:293)

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