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- PDB-3kly: Pentameric formate channel -

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Basic information

Entry
Database: PDB / ID: 3kly
TitlePentameric formate channel
ComponentsPutative formate transporter 1
KeywordsMEMBRANE PROTEIN / channel / formate / Structural Genomics / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


formate transport / 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
Formate transporter 1, putative
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsWaight, A.B. / Wang, D.N. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure and mechanism of a pentameric formate channel
Authors: Waight, A.B. / Love, J. / Wang, D.N.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,56421
Polymers152,8865
Non-polymers4,67816
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24640 Å2
ΔGint-147 kcal/mol
Surface area47800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.795, 101.030, 192.629
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
Putative formate transporter 1


Mass: 30577.186 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_1695 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KRE7
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M TRIS, PH 7.5, 28% (W/V) PEG 550MME, 100MM NACL, 20MM SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC / Detector: CCD / Date: Oct 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 102406 / Observed criterion σ(I): 76.3 / Redundancy: 7.2 % / Rsym value: 0.11 / Net I/σ(I): 12.43

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→33.46 Å / SU ML: 0.23 / σ(F): 0.03 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1593 1.53 %
Rwork0.179 --
obs0.18 102396 90.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.73 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2165 Å20 Å20 Å2
2--0.8785 Å20 Å2
3---4.338 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9793 0 320 346 10459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810358
X-RAY DIFFRACTIONf_angle_d0.99514029
X-RAY DIFFRACTIONf_dihedral_angle_d17.1853754
X-RAY DIFFRACTIONf_chiral_restr0.0731689
X-RAY DIFFRACTIONf_plane_restr0.0041642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.29511250.24968189X-RAY DIFFRACTION81
2.1678-2.24520.25361380.21378633X-RAY DIFFRACTION84
2.2452-2.33510.18561370.1798912X-RAY DIFFRACTION87
2.3351-2.44140.19521400.16369033X-RAY DIFFRACTION89
2.4414-2.570.19821410.15769258X-RAY DIFFRACTION91
2.57-2.7310.17431450.15589534X-RAY DIFFRACTION93
2.731-2.94170.20211600.1589732X-RAY DIFFRACTION95
2.9417-3.23750.20581570.159610004X-RAY DIFFRACTION97
3.2375-3.70550.18211560.167210122X-RAY DIFFRACTION98
3.7055-4.66650.20021490.16859549X-RAY DIFFRACTION92
4.6665-33.46050.23621450.20869431X-RAY DIFFRACTION87
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)
10.1911-0.11290.04640.40620.15680.11130.80750.86441.2471-1.0357-0.1440.28360.7128-0.7811-0.00720.71580.18030.20361.05130.27520.861174.618593.487984.5046
20.3271-0.23870.58610.90270.24281.47980.11780.09920.4912-0.2795-0.20210.0311-0.16520.29870.00020.35190.01450.04180.5580.11710.427856.688777.503498.1561
32.1087-1.3651.20151.6310.82673.5289-0.00711.02220.5235-0.08650.13840.0651-0.2191-0.5648-0.00090.24990.001-0.02010.33210.04240.343856.701575.1512106.971
44.11661.8781.58571.59330.82530.67240.98090.2415-1.31321.15250.493-0.3878-0.73141.52630.06661.0496-0.55520.07671.16820.13340.565571.14993.7562105.0547
50.00460.02870.00810.17540.05610.0137-0.2158-0.40570.0476-0.10040.00861.2153-1.18540.9773-0.0111.0302-0.35180.11231.0999-0.42081.896275.9066101.4032102.2917
60.37390.46390.75410.75771.58543.98240.2513-0.6933-2.2643-0.40621.49580.3065-0.0612.72760.1820.7743-0.44050.10730.91280.24241.125268.565698.602896.6217
71.91840.10460.49571.17920.77642.74020.05620.37810.297-0.1096-0.12740.0309-0.4273-0.3593-0.00010.36690.0355-0.00150.43910.16020.430750.380582.8851101.357
80.2131-0.11890.06811.06020.47690.8039-0.0897-0.32731.0558-0.48351.1605-1.6824-1.00991.57050.02260.4385-0.1620.05760.5390.06520.648775.664378.9225110.0954
92.3807-0.7276-0.05261.2294-0.4221.67770.1170.46750.4155-0.0185-0.0388-0.0179-0.3178-0.2806-00.32890.02020.02570.46860.1470.383148.600282.638102.1431
107.1511-1.797.55124.5806-3.58659.52870.68241.2267-1.0798-1.209-1.0737-2.3221-0.22323.18440.10750.5419-0.4271-0.19340.8960.20981.248873.995694.4546115.7166
110.02240.0356-0.01720.06810.01890.10130.14710.2949-0.1097-0.9629-0.16380.5719-1.9101-1.061300.8398-0.253-0.18980.89040.29371.171381.480998.047128.8011
120.6067-0.96570.45581.5183-0.67712.4402-0.1188-0.02580.50840.0165-0.1085-0.2233-0.41930.2554-00.3718-0.0536-0.01680.28810.00610.416461.25982.2736124.1754
131.213-0.9286-1.06143.1396-1.2242.5467-0.06540.12010.41860.12190.12680.148-0.2425-0.0150.00010.3282-0.0028-0.03990.32670.00770.295359.91172.5222124.175
147.5785-2.75839.04682.803-3.55272.00310.4091-1.6952-0.27380.1511.1258-0.2862-1.1979-0.65010.20360.8796-0.2474-0.12860.5102-0.38521.149374.929581.8056134.9352
150.05850.03220.04870.01380.03640.11311.3652-0.7857-0.0076-0.1358-2.4129-2.1779-0.27450.92890.00831.86240.4121-0.41361.290.32371.569186.290386.9149137.5165
162.00183.17071.99872.6815-1.87912.0029-1.1512-1.2842-0.6540.4188-2.20020.1667-1.0944-0.616-0.46221.5533-0.1099-0.85021.0253-0.21081.004776.776889.3047138.5909
171.5505-1.1517-0.03230.8394-0.23422.1078-0.1189-0.19020.31510.30250.1177-0.0489-0.4292-0.08-00.4578-0.0146-0.08580.2454-0.07660.419656.762581.5338131.6996
180.12310.03040.07350.9515-0.68120.6879-0.4007-0.9826-0.27250.2443-0.05-1.2167-0.71831.8927-0.02170.2403-0.0962-0.00790.71040.06580.655480.157269.3307124.4784
190.87580.201-0.460.85050.47331.955-0.05460.01780.32060.2031-0.0853-0.0111-0.2216-0.0626-0.00010.3942-0.0277-0.06320.2761-0.06720.356455.270680.6479132.3377
200.183-0.0226-0.10860.25160.42960.7737-0.1749-1.0708-0.1642-0.1812-0.4411-2.081-2.63380.55550.01190.56370.0186-0.16891.185-0.07620.921283.941569.6124140.7587
210.4231-0.21050.15570.1058-0.08080.06320.6571-0.5235-0.4678-0.5364-0.0415-0.7245-0.2661-0.76750.00411.35210.0022-0.08651.45540.13181.746298.340958.6978147.0625
220.03160.3514-0.01991.91620.72313.13980.0218-0.3176-0.21770.2303-0.0657-0.17240.12520.2759-0.00020.34240.01280.00560.28420.07190.330566.920157.5138132.3757
230.2493-0.08560.16190.11420.00420.1411-0.071-0.0998-1.18440.14510.9221.8506-0.01151.01940.00040.7898-0.15880.15281.036-0.26430.68879.380748.0674134.5174
240.0509-0.00210.0728-0.0003-0.00090.16190.30560.47040.46840.09260.22830.1917-0.0167-0.73310.03080.8215-0.0018-0.4110.9826-0.24251.383690.796844.9343132.8974
250.0323-0.050.04940.0999-0.11210.1282-0.506-0.24830.5904-0.20240.4975-0.0848-1.25791.3985-0.022.10110.5714-1.16760.9497-0.42143.21791.356742.7248140.8885
260.10350.01230.06720.67-0.0330.0430.41611.4786-2.0623-1.48122.4788-1.96660.32310.55020.00550.70770.1605-0.23231.0242-0.00621.692385.074146.4927142.313
272.1468-0.1174-0.80171.45140.05062.7197-0.1249-0.2881-0.26980.3714-0.04790.14430.27510.00470.00010.42210.0555-0.00110.28520.08660.310863.040752.0143138.9881
280.1727-0.00840.20480.53490.05060.1930.11250.8657-0.3969-0.3823-0.2346-0.57010.44770.4906-0.00150.4420.07780.02230.57690.02350.491278.350156.1284118.8325
291.07520.04130.33761.1416-1.81242.697-0.0096-0.4564-0.09970.24290.05180.1490.173-0.0244-00.4160.01130.00450.28270.08230.381860.666549.6965140.6808
300.4607-0.2527-0.01240.25680.09380.0964-0.1868-0.60111.06751.3662-0.07550.12660.29062.8872-0.01561.41270.48630.16821.13660.01721.374187.941836.5033121.5791
310.17870.26680.25930.35660.40041.2195-0.094-0.422-0.2480.12010.1586-0.32120.81020.6301-0.00210.69150.18350.06080.3995-0.04270.620870.062937.8353116.586
320.4426-0.10680.5470.6794-0.45720.81740.5152-0.9205-0.25350.7119-0.30090.40620.7544-0.86630.0030.5438-0.15890.08010.5325-0.06470.487250.295849.6543112.4953
330.12280.2324-0.32950.3891-0.58151.1246-0.11110.8649-1.1893-0.1312-0.27790.27591.02240.05940.00040.53870.1610.07930.4357-0.08350.498272.284743.0466111.6988
340.13610.10510.11150.11640.09220.0904-0.8797-0.5544-0.15140.6599-1.48930.7720.263-0.5245-0.01212.18591.47210.36792.15240.42790.92883.008636.5073102.2363
350.26510.22580.14780.47430.10280.08541.00240.4607-3.0111-1.4271-0.69971.8901-1.3816-0.10340.03622.95650.85961.25532.15040.31011.96385.585431.06596.3288
362.3206-0.6989-0.99687.3725-4.7376.9075-0.52790.1999-0.0641-0.4383-1.8997-0.02310.20952.0611-0.83681.80020.94520.4681.0987-0.51381.630180.732626.8934102.7074
372.60270.41530.99592.616-0.26421.47230.00220.042-0.535-0.02430.00150.01360.97680.086-0.00010.70120.060.04240.0966-0.09470.492860.226134.9549113.1162
380.16940.0347-0.09660.01970.00110.30750.2964-0.02090.0556-1.36430.5105-1.638-0.61431.535400.65620.07820.24490.8267-0.13270.679178.085152.3859102.0094
391.9356-0.22640.16850.94740.37971.525-0.04210.1215-0.6763-0.0678-0.0365-0.00540.89160.169-0.00360.7620.03120.07310.2364-0.13470.566359.305635.3382111.652
400.8325-0.24510.63640.49320.63772.21070.31781.0365-2.1931-0.41451.2274-0.10942.90330.21790.05770.95880.19310.2891.1386-0.20280.831579.739843.431886.4393
410.20660.0582-0.00020.182-0.15820.1462-0.49950.76341.23620.59120.4893-1.2650.3027-0.5-0.01831.25010.36380.59891.32070.26331.225281.331449.44874.2216
420.4115-0.36280.01181.8806-1.1050.77191.24390.96430.0406-2.8394-0.2546-0.98410.2553-0.64770.02650.87090.07790.32930.8439-0.22480.634173.660749.507179.7639
430.0343-0.20790.12861.2842-0.45490.41610.06191.1911-0.2882-0.432-0.1765-0.110.3252-0.71260.00020.4639-0.01990.02670.5341-0.14090.464357.918651.452295.6695
440.6792-0.48620.34192.3727-0.11880.2850.02410.7844-0.2422-0.0703-0.03630.00980.4252-0.05520.00010.3098-0.0250.02030.5516-0.04960.314957.110458.2481100.2282
450.0287-0.1419-0.07710.6440.22170.3158-0.88221.2616-1.75240.3154-0.07040.0938-0.6249-0.2565-0.00240.7263-0.23520.13931.21460.04020.893375.269964.16778.6282
460.11280.1755-0.13970.366-0.14890.1831-0.5572.39710.103-0.24180.5842-0.7959-1.9984-0.46480.00440.8362-0.11810.04411.34930.05820.57470.25260.690972.7521
471.3305-0.10430.13041.3959-0.03522.7121-0.00940.5999-0.1896-0.27530.02140.06310.3874-0.1305-00.3953-0.04090.0380.5417-0.07810.32455.921656.755792.0153
487.0446-6.0342-2.33695.40743.20496.8429-0.31920.8788-1.32171.28390.7945-0.13541.7734-0.257-0.13970.6501-0.393-0.20180.9002-0.48380.850442.043938.264789.3341
491.1501-1.10041.25541.4666-0.6772.94820.20770.6916-0.3312-0.1070.04880.53320.651-0.667-0.00020.4503-0.1058-0.02380.7209-0.170.342946.848454.897985.6627
501.8915-1.331-0.63511.30730.73360.557-0.00021.5998-2.2997-2.775-0.01870.0443-1.098-0.6134-0.01560.7505-0.2865-0.01781.44850.66761.050972.252680.47983.2584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:31)A22 - 31
2X-RAY DIFFRACTION2(chain A and resid 32:58)A32 - 58
3X-RAY DIFFRACTION3(chain A and resid 59:90)A59 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:99)A91 - 99
5X-RAY DIFFRACTION5(chain A and resid 100:106)A100 - 106
6X-RAY DIFFRACTION6(chain A and resid 107:113)A107 - 113
7X-RAY DIFFRACTION7(chain A and resid 114:178)A114 - 178
8X-RAY DIFFRACTION8(chain A and resid 179:185)A179 - 185
9X-RAY DIFFRACTION9(chain A and resid 186:263)A186 - 263
10X-RAY DIFFRACTION10(chain A and resid 264:278)A264 - 278
11X-RAY DIFFRACTION11(chain B and resid 24:31)B24 - 31
12X-RAY DIFFRACTION12(chain B and resid 32:58)B32 - 58
13X-RAY DIFFRACTION13(chain B and resid 59:88)B59 - 88
14X-RAY DIFFRACTION14(chain B and resid 89:94)B89 - 94
15X-RAY DIFFRACTION15(chain B and resid 95:108)B95 - 108
16X-RAY DIFFRACTION16(chain B and resid 109:113)B109 - 113
17X-RAY DIFFRACTION17(chain B and resid 114:178)B114 - 178
18X-RAY DIFFRACTION18(chain B and resid 179:185)B179 - 185
19X-RAY DIFFRACTION19(chain B and resid 186:266)B186 - 266
20X-RAY DIFFRACTION20(chain B and resid 267:278)B267 - 278
21X-RAY DIFFRACTION21(chain C and resid 20:27)C20 - 27
22X-RAY DIFFRACTION22(chain C and resid 28:88)C28 - 88
23X-RAY DIFFRACTION23(chain C and resid 89:94)C89 - 94
24X-RAY DIFFRACTION24(chain C and resid 95:100)C95 - 100
25X-RAY DIFFRACTION25(chain C and resid 101:108)C101 - 108
26X-RAY DIFFRACTION26(chain C and resid 109:113)C109 - 113
27X-RAY DIFFRACTION27(chain C and resid 114:178)C114 - 178
28X-RAY DIFFRACTION28(chain C and resid 179:194)C179 - 194
29X-RAY DIFFRACTION29(chain C and resid 195:270)C195 - 270
30X-RAY DIFFRACTION30(chain C and resid 271:279)C271 - 279
31X-RAY DIFFRACTION31(chain D and resid 27:58)D27 - 58
32X-RAY DIFFRACTION32(chain D and resid 59:72)D59 - 72
33X-RAY DIFFRACTION33(chain D and resid 73:90)D73 - 90
34X-RAY DIFFRACTION34(chain D and resid 91:96)D91 - 96
35X-RAY DIFFRACTION35(chain D and resid 97:106)D97 - 106
36X-RAY DIFFRACTION36(chain D and resid 107:113)D107 - 113
37X-RAY DIFFRACTION37(chain D and resid 114:178)D114 - 178
38X-RAY DIFFRACTION38(chain D and resid 179:185)D179 - 185
39X-RAY DIFFRACTION39(chain D and resid 186:271)D186 - 271
40X-RAY DIFFRACTION40(chain D and resid 272:278)D272 - 278
41X-RAY DIFFRACTION41(chain E and resid 23:28)E23 - 28
42X-RAY DIFFRACTION42(chain E and resid 29:34)E29 - 34
43X-RAY DIFFRACTION43(chain E and resid 35:58)E35 - 58
44X-RAY DIFFRACTION44(chain E and resid 59:88)E59 - 88
45X-RAY DIFFRACTION45(chain E and resid 89:105)E89 - 105
46X-RAY DIFFRACTION46(chain E and resid 106:113)E106 - 113
47X-RAY DIFFRACTION47(chain E and resid 114:222)E114 - 222
48X-RAY DIFFRACTION48(chain E and resid 223:228)E223 - 228
49X-RAY DIFFRACTION49(chain E and resid 229:270)E229 - 270
50X-RAY DIFFRACTION50(chain E and resid 271:279)E271 - 279

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