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- PDB-6b24: Crystal structure of fluoride channel Fluc Ec2 F80Y Mutant -

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Basic information

Entry
Database: PDB / ID: 6b24
TitleCrystal structure of fluoride channel Fluc Ec2 F80Y Mutant
Components
  • Fluoride ion transporter CrcB
  • monobody
KeywordsTRANSPORT PROTEIN / alpha helix / ion channel / membrane protein
Function / homology
Function and homology information


fluoride channel activity / cellular detoxification of fluoride / metal ion binding / plasma membrane
Similarity search - Function
Putative fluoride ion transporter CrcB / CrcB-like protein, Camphor Resistance (CrcB) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FLUORIDE ION / Fluoride-specific ion channel FluC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLast, N.B. / Sun, S. / Pham, M.C. / Miller, C.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107023 United States
CitationJournal: Elife / Year: 2017
Title: Molecular determinants of permeation in a fluoride-specific ion channel.
Authors: Last, N.B. / Sun, S. / Pham, M.C. / Miller, C.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluoride ion transporter CrcB
B: Fluoride ion transporter CrcB
C: monobody
D: monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,44612
Polymers47,9004
Non-polymers1,5478
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-72 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.400, 88.400, 146.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELEULEUAA2 - 1242 - 124
21ILEILELEULEUBB2 - 1242 - 124
12SERSERTHRTHRCC1 - 961 - 96
22SERSERTHRTHRDD1 - 961 - 96

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Fluoride ion transporter CrcB


Mass: 13631.307 Da / Num. of mol.: 2 / Mutation: R25K, F80Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: crcB, A4T40_27000, AC789_145pl00540, AKG99_27195, BET08_05210, BK251_13005, BK292_28205, BK334_22235, BK373_23795, BUE82_27975, ECONIH1_26550, ECS286_0026, MJ49_27125, pCTXM15_EC8_00123, pO103_22
Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6J5N4
#2: Protein monobody


Mass: 10318.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHFT2 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 1 types, 3 molecules

#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 3 types, 16 molecules

#4: Chemical
ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: F
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 5.98 Å3/Da / Density % sol: 79.42 % / Mosaicity: 0 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.2
Details: 30% PEG 600, 100 mM ADA, 10 mM HEPES, 100 mM NaF, 50 mM LiNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2016
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→42.65 Å / Num. obs: 27945 / % possible obs: 95.9 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.034 / Rrim(I) all: 0.111 / Net I/σ(I): 11.2 / Num. measured all: 282249 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.99.51.32541110.7140.441.39997.2
8.7-42.6510.30.0448690.9970.0140.04691.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KBN

5kbn


Resolution: 2.75→42.65 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.882 / SU B: 30.446 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.258
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1382 4.9 %RANDOM
Rwork0.2253 ---
obs0.2267 26553 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.59 Å2 / Biso mean: 93.517 Å2 / Biso min: 68.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.89 Å20 Å20 Å2
2---4.89 Å20 Å2
3---9.78 Å2
Refinement stepCycle: final / Resolution: 2.75→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 104 11 3477
Biso mean--109.25 92.34 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193554
X-RAY DIFFRACTIONr_bond_other_d0.0010.023391
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9674869
X-RAY DIFFRACTIONr_angle_other_deg0.84737859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80922.745102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04815523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.191156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A77120.03
12B77120.03
21C55120.05
22D55120.05
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 105 -
Rwork0.372 1972 -
all-2077 -
obs--97.15 %
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)
18.44140.08260.35121.5549-0.3471.5283-0.07090.41170.71250.00070.09490.1705-0.0763-0.0667-0.0240.02080.03760.02550.22790.03970.183238.3334184.54619.1005
27.13470.4852-1.4322.1112-0.2592.581-0.26421.0369-0.6096-0.27760.1722-0.1470.13510.07750.09210.06560.02160.05230.3983-0.07080.12544.8132173.50283.5263
36.98032.1772-4.40932.4718-2.01995.8885-0.11070.4533-0.35080.10740.09730.10190.2266-0.25120.01340.04550.00820.02730.07190.04570.2128.7242168.15720.7013
411.5712-0.95841.69990.8478-0.89171.7381-0.0933-0.05730.26990.03990.0596-0.0422-0.1393-0.02750.03370.0240.02390.03030.1502-0.0170.195978.4796183.76369.461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 125
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3C1 - 96
4X-RAY DIFFRACTION4D1 - 96

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