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- PDB-3kcu: Structure of formate channel -

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Basic information

Entry
Database: PDB / ID: 3kcu
TitleStructure of formate channel
ComponentsProbable formate transporter 1
KeywordsTRANSPORT PROTEIN / TCDB ID 2.A.44.1.1 / Transporter / Channel / Formate / Cell inner membrane / Cell membrane / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


formate transmembrane transporter activity / identical protein binding / plasma membrane
Similarity search - Function
Formate transporter FocA, putative / Formate and nitrite transporters signature 1. / Formate and nitrite transporters signature 2. / Formate/nitrite transporter / Formate/nitrite transporter, conserved site / Formate/nitrite transporter / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MA5 / Formate channel FocA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.243 Å
AuthorsWang, Y. / Huang, Y. / Wang, J. / Yan, N. / Shi, Y.
CitationJournal: Nature / Year: 2009
Title: Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel
Authors: Wang, Y. / Huang, Y. / Wang, J. / Cheng, C. / Huang, W. / Lu, P. / Xu, Y.-N. / Wang, P. / Yan, N. / Shi, Y.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable formate transporter 1
B: Probable formate transporter 1
C: Probable formate transporter 1
D: Probable formate transporter 1
E: Probable formate transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5166
Polymers155,0635
Non-polymers4521
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15630 Å2
ΔGint-209 kcal/mol
Surface area43990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.378, 107.934, 163.128
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
Probable formate transporter 1 / Formate efflux permease / Formate channel 1


Mass: 31012.605 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: FOCA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC25
#2: Chemical ChemComp-MA5 / 2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL / CYCLOHEXYLETHYL-BETA-D-MALTOSIDE


Mass: 452.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O11
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MOPS, pH 7.5, 36% (w/v) PEG 400, 200mM NaCl or sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.243→39.989 Å / Num. obs: 85366 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 50.48 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.243→39.989 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.832 / SU ML: 0.28 / Isotropic thermal model: TLS / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4365 5.13 %Thin Shell
Rwork0.203 80784 --
obs0.205 85149 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.125 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 264.7 Å2 / Biso mean: 72.399 Å2 / Biso min: 30.35 Å2
Baniso -1Baniso -2Baniso -3
1--4.811 Å20 Å2-0 Å2
2--12.461 Å20 Å2
3----7.65 Å2
Refinement stepCycle: LAST / Resolution: 2.243→39.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9458 0 31 104 9593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089786
X-RAY DIFFRACTIONf_angle_d0.99513343
X-RAY DIFFRACTIONf_chiral_restr0.0731594
X-RAY DIFFRACTIONf_plane_restr0.0051600
X-RAY DIFFRACTIONf_dihedral_angle_d15.4563242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Num. reflection all
2.243-2.26900.28225180
2.269-2.2960.2786510.2522160982811
2.296-2.32300.234275999
2.323-2.35300.212284999
2.353-2.38400.219279899
2.384-2.41700.2172855100
2.417-2.4510.2475960.20822291002825
2.451-2.48800.1992812100
2.488-2.52600.1952861100
2.526-2.56800.1992813100
2.568-2.6120.2535630.18722921002855
2.612-2.6600.1882843100
2.66-2.71100.1892856100
2.711-2.7660.2671600.18326841002844
2.766-2.8260.2423520.18825021002854
2.826-2.89200.1792856100
2.892-2.96400.1842849100
2.964-3.0440.2214840.17523571002841
3.044-3.13400.1722874100
3.134-3.23500.1792869100
3.235-3.3510.2234280.18324401002868
3.351-3.48500.1982906100
3.485-3.64300.1772850100
3.643-3.8350.2253770.18325071002884
3.835-4.07500.1972907100
4.075-4.38900.192886100
4.389-4.8310.2293410.20125711002912
4.831-5.52800.22291899
5.528-6.9590.2862540.242687992941
6.959-39.9950.1691590.2212743932902
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)
10.26480.0123-0.48830.8240.08142.35230.08090.14140.0159-0.0535-0.0171-0.0835-0.01580.184-0.05020.22480.03630.01180.36120.03820.286841.003520.7846145.5572
20.4011-0.4224-0.58651.3431-0.582.48120.1758-0.1290.16370.09210.005-0.0342-0.20020.3276-0.17030.3243-0.0580.00320.4597-0.03860.421340.681427.4654173.5821
30.5558-0.1910.25070.6924-0.0142.49090.0347-0.4444-0.04820.23110.01360.03470.66220.1304-0.04860.59820.0639-0.05040.58260.10820.369438.00543.9993188.4811
40.9244-0.1389-0.25880.0180.02981.82290.0877-0.0875-0.39980.098-0.07220.12391.5399-0.031-0.02121.40480.0998-0.03560.35560.10310.541438.0233-18.7994170.403
50.26410.21390.10190.7613-0.07092.91750.06980.1916-0.1425-0.08850.00460.01341.25870.1437-0.06160.88810.1298-0.02730.4336-0.07540.390939.3988-8.0069143.4729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA29 - 280
2X-RAY DIFFRACTION2chain BB29 - 280
3X-RAY DIFFRACTION3chain CC29 - 276
4X-RAY DIFFRACTION4chain DD29 - 276
5X-RAY DIFFRACTION5chain EE30 - 278

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