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- PDB-5kom: The crystal structure of fluoride channel Fluc Ec2 F83I Mutant -

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Basic information

Entry
Database: PDB / ID: 5kom
TitleThe crystal structure of fluoride channel Fluc Ec2 F83I Mutant
Components
  • Putative 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 / molecular replacement / Resolution: 2.69 Å
AuthorsLast, N.B. / Kolmakova-Partensky, L. / Shane, T. / Miller, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1-GM107023 United States
CitationJournal: Elife / Year: 2016
Title: Mechanistic signs of double-barreled structure in a fluoride ion channel.
Authors: Last, N.B. / Kolmakova-Partensky, L. / Shane, T. / Miller, C.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / 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 / _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: Putative fluoride ion transporter CrcB
B: Putative fluoride ion transporter CrcB
C: monobody
D: monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,87710
Polymers52,3694
Non-polymers1,5096
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-62 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.500, 87.500, 144.540
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: 0 / Refine code: 0

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 - 962 - 97
22SERSERTHRTHRDD1 - 962 - 97

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Putative fluoride ion transporter CrcB


Mass: 15808.770 Da / Num. of mol.: 2 / Mutation: R25K, F83I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: crcB, AC789_145pl00540, AKG99_27195, AL505_410006, AN206_26275, AUQ25_20445, ECONIH1_26550, ECS286_0026, MJ49_27125, pCTXM15_EC8_00123, pO103_22, SK78_04822
Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6J5N4
#2: Protein monobody /


Mass: 10375.529 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 (E. coli) / Strain (production host): BL21(DE3)

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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, 12 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 / Fluoride


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 5.28 Å3/Da / Density % sol: 76.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 36% 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: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2015
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.69→38.01 Å / Num. obs: 30195 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.69-2.827.51.0371100
8.92-38.017.30.02197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASERphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A43
Resolution: 2.69→38.01 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.909 / SU B: 21.365 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.218
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1455 4.8 %RANDOM
Rwork0.217 ---
obs0.2177 28695 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 152.63 Å2 / Biso mean: 75.044 Å2 / Biso min: 52.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å20 Å2
2---2.49 Å20 Å2
3---4.97 Å2
Refinement stepCycle: final / Resolution: 2.69→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 102 9 3465
Biso mean--91.88 67.2 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193544
X-RAY DIFFRACTIONr_bond_other_d0.0020.023445
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9684855
X-RAY DIFFRACTIONr_angle_other_deg0.93237951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12622.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65815525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.694156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213747
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02751
X-RAY DIFFRACTIONr_mcbond_it1.4024.3891760
X-RAY DIFFRACTIONr_mcbond_other1.4014.3891759
X-RAY DIFFRACTIONr_mcangle_it2.3736.582193
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A362500.03
12B362500.03
21C262780.08
22D262780.08
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 119 -
Rwork0.331 2097 -
all-2216 -
obs--99.77 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2017-0.8506-0.67338.70192.07492.2680.17890.2689-0.1958-1.1605-0.2650.5632-0.0523-0.21950.08610.4187-0.0216-0.09370.0583-0.06710.346484.084443.3973-19.3734
21.9307-0.1418-0.59889.0359-0.17391.71970.1209-0.01930.203-0.5031-0.0657-0.8847-0.03050.0387-0.05520.2801-0.02980.04450.011-0.03240.379695.048249.8553-14.0091
31.9050.1516-0.638412.8405-2.26241.98570.0170.0258-0.14210.2722-0.0845-0.2072-0.12730.1640.06750.2716-0.0111-0.02290.0196-0.0180.327994.32779.9764-13.5246
42.8187-2.6971-2.01758.23895.4166.35550.0818-0.12780.1638-0.4575-0.06340.1922-0.2591-0.2359-0.01840.1251-0.01330.0480.0481-0.04080.390278.780179.042-2.4908
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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