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- PDB-6b2d: Crystal structure of fluoride channel Fluc Ec2 T114S Mutant -

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Basic information

Entry
Database: PDB / ID: 6b2d
TitleCrystal structure of fluoride channel Fluc Ec2 T114S 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: 3.01 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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_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

Downloads & links

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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)49,36711
Polymers47,8404
Non-polymers1,5287
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-71 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.090, 87.090, 143.870
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: 13601.280 Da / Num. of mol.: 2 / Mutation: R25K, T114S
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, 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

#4: 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, 10 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: F
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 5.7 Å3/Da / Density % sol: 78.43 % / Mosaicity: 0 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 31% 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: 8.2.1 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.01→37.84 Å / Num. obs: 21243 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.036 / Rrim(I) all: 0.106 / Net I/σ(I): 14.1 / Num. measured all: 185752 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.01-3.198.91.4753017733920.7070.5231.5661.599.6
9.03-37.848.40.03167008010.9990.0110.03357.697.9

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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: 3.01→37.84 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.876 / SU B: 40.665 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1062 5 %RANDOM
Rwork0.2377 ---
obs0.2385 20151 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.07 Å2 / Biso mean: 108.664 Å2 / Biso min: 81.44 Å2
Baniso -1Baniso -2Baniso -3
1--5.75 Å20 Å20 Å2
2---5.75 Å20 Å2
3---11.49 Å2
Refinement stepCycle: final / Resolution: 3.01→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 100 6 3464
Biso mean--126.01 102.74 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193547
X-RAY DIFFRACTIONr_bond_other_d0.0010.023381
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.9664858
X-RAY DIFFRACTIONr_angle_other_deg0.837835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86522.745102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60415523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.053156
X-RAY DIFFRACTIONr_chiral_restr0.0540.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A78200.04
12B78200.04
21C56860.08
22D56860.08
LS refinement shellResolution: 3.01→3.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 90 -
Rwork0.385 1443 -
all-1533 -
obs--99.67 %
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)
12.4826-0.44350.43317.9447-1.65112.67570.19530.24570.2545-1.2715-0.4259-0.8549-0.05230.27370.23060.5168-0.00580.1350.06970.06670.11183.378943.628111.091
21.86810.1560.58448.80051.16282.20620.10890.0079-0.2441-0.4292-0.12280.96360.0234-0.0270.01390.3386-0.0002-0.04350.0118-0.00460.1552-7.752536.937916.7061
31.73760.370.874710.69530.95342.2569-0.0065-0.06580.05460.0166-0.08640.29350.0489-0.00120.09290.2122-0.01320.00270.06640.00830.0604-6.939276.706117.35
43.5723-3.15721.407810.7641-6.27636.79090.0875-0.2004-0.0375-0.681-0.0553-0.50920.32450.2963-0.03220.1023-0.029-0.00010.1148-0.0090.14948.78348.142228.1422
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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