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- PDB-6bx5: The crystal structure of fluoride channel Fluc Ec2 with Monobody S12 -

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Basic information

Entry
Database: PDB / ID: 6bx5
TitleThe crystal structure of fluoride channel Fluc Ec2 with Monobody S12
Components
  • Monobody S12
  • Putative fluoride ion transporter CrcB
KeywordsTRANSPORT PROTEIN / Fluc / Fluoride channel / monobody
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: 3 Å
AuthorsTurman, D.L. / Miller, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM10723 United States
CitationJournal: Biochemistry / Year: 2018
Title: Molecular Interactions between a Fluoride Ion Channel and Synthetic Protein Blockers.
Authors: Turman, D.L. / Cheloff, A.Z. / Corrado, A.D. / Nathanson, J.T. / Miller, C.
History
DepositionDec 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 S12
D: Monobody S12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8489
Polymers47,7494
Non-polymers995
Water36020
1
A: Putative fluoride ion transporter CrcB
C: Monobody S12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9556
Polymers23,8752
Non-polymers804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative fluoride ion transporter CrcB
D: Monobody S12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8943
Polymers23,8752
Non-polymers191
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.441, 105.441, 183.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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
11METMETPHEPHEAA1 - 1251 - 125
21METMETPHEPHEBB1 - 1251 - 125
12SERSERARGARGCC3 - 963 - 96
22SERSERARGARGDD3 - 963 - 96

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative fluoride ion transporter CrcB / Fluoride channel (Fluc) homolog Ec2


Mass: 13544.229 Da / Num. of mol.: 2 / Mutation: R25K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: crcB, A4T40_27000, A8M81_25235, AC789_145pl00540, AKG99_27195, B7C53_24430, BET08_05210, BIU72_24510, BK292_28205, BK334_22235, BK373_23795, BMR46_27175, BMR58_00505, BMR59_25090, BMR61_25795, ...Gene: crcB, A4T40_27000, A8M81_25235, AC789_145pl00540, AKG99_27195, B7C53_24430, BET08_05210, BIU72_24510, BK292_28205, BK334_22235, BK373_23795, BMR46_27175, BMR58_00505, BMR59_25090, BMR61_25795, CDL37_21115, CNQ53_00195, ECONIH1_26550, ECS286_0026, MJ49_27125, pCTXM15_EC8_00123, pO103_22
Production host: Escherichia coli (E. coli) / References: UniProt: Q6J5N4
#2: Protein Monobody S12


Mass: 10330.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Engineered human fibronectin type III domain / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-F / FLUORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 50 mM ADA-NaOH, 50 mM LiNO3, 34% PEG 400

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 3→91.53 Å / Num. obs: 21435 / % possible obs: 100 % / Redundancy: 28.1 % / CC1/2: 1 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.031 / Rrim(I) all: 0.165 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.1829.11.98333800.8420.3722.018100
9-91.51250.02892510.0060.02999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å91.36 Å
Translation3 Å91.36 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kbn

5kbn


Resolution: 3→91.53 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.846 / SU B: 25.255 / SU ML: 0.216 / SU R Cruickshank DPI: 0.4828 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.311
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1077 5 %RANDOM
Rwork0.2233 ---
obs0.2247 20295 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.19 Å2 / Biso mean: 85.372 Å2 / Biso min: 46.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2--1.96 Å20 Å2
3----3.91 Å2
Refinement stepCycle: final / Resolution: 3→91.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 5 20 3386
Biso mean--79.66 68.3 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023453
X-RAY DIFFRACTIONr_bond_other_d0.0020.023283
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.9644734
X-RAY DIFFRACTIONr_angle_other_deg1.11637578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37722.885104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79915516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.306156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02724
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A81300.1
12B81300.1
21C55940.11
22D55940.11
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 85 -
Rwork0.3 1433 -
all-1518 -
obs--100 %
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)
14.4424-4.6821-2.53658.07464.56467.1997-0.1884-0.09150.0280.38880.05510.0282-0.0932-0.20380.13330.12810.11470.02050.15040.07580.118626.447-27.363196.229
26.8431-3.9346-0.47755.58741.8933.99870.38110.18770.8278-0.5239-0.043-1.27-0.39820.4047-0.3380.27640.09730.13040.18020.04910.38536.678-24.097187.561
35.3765-3.8568-4.14377.60597.196610.1506-0.32790.0601-0.22820.01750.18580.2564-0.06830.03060.14220.05280.01690.0240.07030.0430.052645.121-54.425174.741
410.8188-5.7163-0.68526.16920.76754.21930.5075-0.01010.5039-0.3271-0.2982-0.1502-0.9086-0.6787-0.20930.63310.4320.03750.34480.03040.09156.299-0.015194.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3C1 - 97
4X-RAY DIFFRACTION4D3 - 97

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