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- PDB-3te2: Crystal structure of HSC K16S -

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Basic information

Entry
Database: PDB / ID: 3te2
TitleCrystal structure of HSC K16S
Componentsformate/nitrite transporter
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


formate transmembrane transporter activity / membrane / metal ion binding
Similarity search - Function
Formate and nitrite transporters signature 1. / 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/nitrite transporter
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsCzyzewski, B.K. / Wang, D.-N.
CitationJournal: Nature / Year: 2012
Title: Identification and characterization of a bacterial hydrosulphide ion channel.
Authors: Czyzewski, B.K. / Wang, D.N.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: formate/nitrite transporter
B: formate/nitrite transporter
C: formate/nitrite transporter
D: formate/nitrite transporter
E: formate/nitrite transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,14417
Polymers141,1275
Non-polymers3,01812
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21890 Å2
ΔGint-135 kcal/mol
Surface area40340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.689, 118.704, 150.672
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
formate/nitrite transporter


Mass: 28225.340 Da / Num. of mol.: 5 / Mutation: K16S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_22300, Putative formate/nitrite transporter / Plasmid: pBad / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q186B7
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: 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.: 7
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9 / Details: PEG 400, pH 9.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 79396 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.345.90.804199.9
2.34-2.3870.7261100
2.38-2.437.30.621100
2.43-2.487.30.5831100
2.48-2.537.30.5251100
2.53-2.597.30.4571100
2.59-2.667.30.4141100
2.66-2.737.30.3591100
2.73-2.817.30.3081100
2.81-2.97.30.2741100
2.9-37.30.2331100
3-3.127.30.2021100
3.12-3.267.30.1681100
3.26-3.447.30.1361100
3.44-3.657.20.1131100
3.65-3.9370.0941100
3.93-4.336.80.078199.9
4.33-4.956.80.071100
4.95-6.2470.0731100
6.24-506.30.055197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLY
Resolution: 2.3→32.14 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.62 / σ(F): 1.33 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 3976 5.02 %
Rwork0.185 --
obs0.187 79241 99.8 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.74 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 45.29 Å2
Baniso -1Baniso -2Baniso -3
1--5.0207 Å2-0 Å20 Å2
2---1.6095 Å2-0 Å2
3---6.6302 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9543 0 205 335 10083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049925
X-RAY DIFFRACTIONf_angle_d0.95913413
X-RAY DIFFRACTIONf_dihedral_angle_d13.8883617
X-RAY DIFFRACTIONf_chiral_restr0.1861695
X-RAY DIFFRACTIONf_plane_restr0.0031586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2975-2.32550.32651270.26072599X-RAY DIFFRACTION98
2.3255-2.35490.3011430.23762649X-RAY DIFFRACTION100
2.3549-2.38590.2671360.21992682X-RAY DIFFRACTION100
2.3859-2.41850.24141410.20052673X-RAY DIFFRACTION100
2.4185-2.45310.28331370.18952666X-RAY DIFFRACTION100
2.4531-2.48970.23611360.20122653X-RAY DIFFRACTION100
2.4897-2.52860.26841540.19752671X-RAY DIFFRACTION100
2.5286-2.570.24731370.17422656X-RAY DIFFRACTION100
2.57-2.61430.22421160.18862684X-RAY DIFFRACTION100
2.6143-2.66180.2481670.18532642X-RAY DIFFRACTION100
2.6618-2.7130.23931240.18562659X-RAY DIFFRACTION100
2.713-2.76840.26491540.19042672X-RAY DIFFRACTION100
2.7684-2.82850.28551400.19052666X-RAY DIFFRACTION100
2.8285-2.89430.24261500.18312682X-RAY DIFFRACTION100
2.8943-2.96660.28131370.19012674X-RAY DIFFRACTION100
2.9666-3.04670.24151420.19392671X-RAY DIFFRACTION100
3.0467-3.13630.21691250.18512691X-RAY DIFFRACTION100
3.1363-3.23750.24741370.18772673X-RAY DIFFRACTION100
3.2375-3.35310.2221450.17792713X-RAY DIFFRACTION100
3.3531-3.48720.2211510.1782680X-RAY DIFFRACTION100
3.4872-3.64570.20721490.17892691X-RAY DIFFRACTION100
3.6457-3.83760.23671440.17442708X-RAY DIFFRACTION100
3.8376-4.07760.17861500.16832701X-RAY DIFFRACTION100
4.0776-4.39170.19051350.15632722X-RAY DIFFRACTION100
4.3917-4.83230.20121600.16772708X-RAY DIFFRACTION100
4.8323-5.52850.21461560.18092748X-RAY DIFFRACTION100
5.5285-6.95370.27831450.20182776X-RAY DIFFRACTION100
6.9537-32.14240.21361380.19542855X-RAY DIFFRACTION98
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)
10.70390.2451-0.05183.75831.2771.42870.02250.1229-0.1387-0.3170.0138-0.52570.28240.19260.08690.5546-0.03590.26290.4131-0.06380.335326.701225.2048-10.081
20.9799-0.0391-0.22721.81270.46811.2363-0.02840.06530.019-0.1446-0.01920.2344-0.0333-0.0550.03540.1459-0.0286-0.00970.2076-0.0430.19979.080318.83986.8597
31.02950.1276-0.49231.1371-0.37431.00720.0710.2721-0.0896-0.5257-0.0385-0.0725-0.22420.12170.03250.4324-0.0736-0.00150.3324-0.09930.134713.425917.7903-8.9135
42.0921-1.45191.30442.3302-1.02592.7102-0.0625-0.1277-0.0875-0.18390.11980.70940.0368-0.59620.07710.1906-0.0571-0.10760.3309-0.06380.4598-6.530316.42726.8444
50.43040.26780.42931.36780.48520.7708-0.01560.2149-0.0522-0.47410.01680.1114-0.09040.0597-0.00720.1929-0.0138-0.04860.2437-0.01710.15649.319926.70191.2563
64.047-0.41211.01520.37-0.34851.1478-0.1325-0.1817-0.1251-0.04860.08130.181-0.0192-0.1626-0.36040.1232-0.022-0.04980.4033-0.08730.5119-9.12919.62492.882
71.57221.10210.00871.40590.05010.5915-0.04120.3441-0.0864-0.20420.1270.204-0.0149-0.01610.25150.381-0.0389-0.26060.2928-0.02990.24131.440522.4243-8.9232
82.6563-0.97730.0654.9062-0.0575.65550.02240.45750.0201-0.56030.2136-0.2911-0.08030.3135-0.19040.6351-0.09840.09470.3771-0.00540.191920.181936.9433-12.7375
91.82050.04481.52771.2347-0.13956.0685-0.13360.1732-0.0824-0.30840.2663-0.15230.25180.25270.01650.2615-0.05890.17160.3029-0.0310.26632.098651.82321.6379
101.35380.4813-0.27641.8562-0.00321.8269-0.02510.09350.1515-0.2066-0.04430.3446-0.116-0.19430.00350.18970.0263-0.05580.2106-0.00790.21159.631941.61476.2244
111.3147-1.0712-0.12270.892-0.00292.10160.10960.0760.1154-0.4190.1311-0.0724-0.2895-0.0686-0.28080.3127-0.01260.07270.25980.01970.266226.545757.86962.6914
122.66561.13940.23761.78450.5030.7387-0.02320.59440.1645-0.56140.12320.2026-0.038-0.109-0.07960.38850.0324-0.12230.2160.07280.194112.051950.9014-4.7294
130.8656-0.8495-0.30341.1055-0.04940.54830.02490.01350.0047-0.21190.03750.56390.0397-0.170.00470.18390.089-0.18040.3301-0.03670.6004-5.229346.75217.3314
140.79710.14990.20151.45310.10970.430.0250.10080.1467-0.3148-0.0510.0617-0.07080.0572-0.02890.21660.017-0.01730.2122-0.01750.210313.951948.874210.9384
152.59490.53690.67610.15440.30930.8418-0.0613-0.00260.1347-0.0963-0.01730.2176-0.1073-0.19750.06740.39510.0971-0.2870.5953-0.04020.9202-8.726949.25540.3836
163.43890.10190.30031.22-0.17950.74940.2140.11310.3466-0.3439-0.21070.1583-0.1779-0.26590.0540.36590.0968-0.08930.24810.04560.37538.116259.42874.6573
172.7510.96430.19074.6634-0.56234.90460.25110.21880.0978-0.0720.0071-0.4798-0.19520.2557-0.11250.2442-0.05230.08060.2465-0.0590.336331.190960.528412.349
181.01940.22610.78420.44770.5131.2679-0.19220.17370.42240.1721-0.0122-0.2687-0.30880.2101-0.70210.3485-0.0266-0.46960.38070.02920.662844.120819.162533.9453
190.46590.15370.20540.95960.44660.5490.0726-0.4204-0.1450.86390.0873-0.5280.25450.24060.13150.50480.0062-0.41140.25150.0241-0.04128.281427.525542.1175
200.97650.05110.08640.7039-0.56420.56180.0893-0.49550.05030.31360.09480.0926-0.0071-0.00020.03220.7946-0.14770.13260.4528-0.01750.136311.351630.244150.4395
210.9506-0.690.21940.7282-0.31121.45490.0216-0.2733-0.19950.5739-0.058-0.31660.30730.21840.04510.3751-0.029-0.0960.22990.01730.202724.867419.27133.9428
221.355-0.16790.74723.90860.25921.7425-0.1376-0.6380.13670.63910.0620.2891-0.2357-0.1336-0.16010.8948-0.03-0.04830.5173-0.02450.222318.732328.554951.6451
230.5602-0.0727-0.42190.60430.23360.90760.0164-0.3402-0.12320.52630.048-0.10730.03480.0994-0.18720.75130.0542-0.30820.38690.11870.290529.119213.85344.6445
246.1742-2.0662.93290.7594-0.55334.08720.00260.10470.222-0.0197-0.0689-0.1415-0.042-0.02550.16660.4213-0.0298-0.29330.60190.17390.886645.2365-0.582531.2036
251.7969-1.87341.97853.2395-3.06925.3747-0.18410.08430.0610.1876-0.0934-0.7229-0.11050.59620.19590.19550.06990.01670.3263-0.04120.565833.7365.15710.0632
261.8523-0.1440.20671.99840.20491.90660.123-0.0178-0.05980.4693-0.08270.06390.2359-0.141-0.06880.2471-0.05420.01480.17820.01970.189516.986412.223127.1476
271.37540.35920.23021.8861-1.11380.8248-0.0330.1324-0.404-0.04020.0371-0.31530.31550.1573-0.02340.24110.04680.00120.2531-0.02670.422727.3793-0.09789.7677
282.0510.549-0.36320.62970.76872.52360.0585-0.248-0.53060.5837-0.0589-0.29160.01580.2141-0.1290.4830.0208-0.05750.19910.10380.35822.9489-1.070626.8988
290.91950.38920.00391.0970.07020.72750.0746-0.213-0.10180.3682-0.14750.1391-0.12560.01040.19770.5526-0.15380.23520.24280.01160.34243.90816.204133.4539
300.79310.2281-0.25761.49240.04991.10950.3357-0.0946-0.26640.3857-0.2055-0.17340.0270.14140.00990.1341-0.01320.03870.1386-0.02280.217314.27026.073912.9276
310.18070.12140.49131.88690.43061.3349-0.0184-0.14410.07120.10060.0663-0.19750.05790.244-0.0530.14890.0120.02390.2138-0.00950.200219.213818.471715.5829
321.8236-0.12730.01820.50850.62231.28020.0092-0.1354-0.24720.7088-0.15470.00920.093-0.0723-0.04220.4321-0.0390.03990.23020.05870.233111.90093.119527.8639
332.05390.24861.2452.44872.78493.62450.1332-0.25350.18580.3161-0.01250.4951-0.2626-0.1967-0.05560.9042-0.18220.22930.46340.15230.60664.1226-0.55938.4835
343.93141.5353-2.73562.915-1.77412.96420.01180.0465-0.52340.3355-0.14960.10490.0545-0.05550.10890.3293-0.00720.08480.195-0.01030.393212.2705-3.189218.8783
351.9744-0.92942.26523.8488-0.35782.894-0.03030.6242-0.3434-0.5306-0.0541-0.67160.41890.58510.3290.33080.00010.11950.3609-0.10180.334624.89874.3495-0.2839
360.74120.15920.23252.05490.03810.92890.0141-0.13080.11920.2727-0.0035-0.275-0.03750.0724-0.04660.1946-0.0002-0.030.1637-0.07080.211724.669249.176227.4793
370.34880.4414-0.15810.71030.06570.48390.0126-0.18670.16350.28630.0422-0.3613-0.10590.15370.05770.22310.0055-0.06880.245-0.1360.383730.11155.112630.0169
381.03570.54040.69621.12360.21745.51980.0856-0.10940.15020.2658-0.08050.41810.1663-0.42920.02260.2696-0.00530.14670.298-0.1280.40275.681755.183234.112
390.57070.20980.21880.94640.14131.22080.0648-0.0930.04430.3997-0.0471-0.36530.14150.1029-0.01620.218-0.0326-0.04560.2414-0.07010.210922.814445.527333.6656
401.27320.05340.25740.2029-0.31050.56740.04180.07230.02470.0109-0.06680.0931-0.1487-0.33390.34760.46790.23970.23630.6267-0.13170.7324.737363.383535.2891
412.501-0.9831-0.61850.9361-0.2760.64950.2362-0.26160.15420.33840.0082-0.1375-0.04050.070.28240.4773-0.0823-0.04210.3361-0.2090.25822.607456.426641.765
422.35541.07250.87171.38190.4852.83750.03890.0522-0.16410.17960.1342-0.45230.14750.62040.0620.42340.0623-0.37550.4143-0.08540.498841.852941.592440.8779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:23)
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:82)
3X-RAY DIFFRACTION3chain 'A' and (resseq 83:129)
4X-RAY DIFFRACTION4chain 'A' and (resseq 130:152)
5X-RAY DIFFRACTION5chain 'A' and (resseq 153:214)
6X-RAY DIFFRACTION6chain 'A' and (resseq 215:222)
7X-RAY DIFFRACTION7chain 'A' and (resseq 223:242)
8X-RAY DIFFRACTION8chain 'A' and (resseq 243:256)
9X-RAY DIFFRACTION9chain 'B' and (resseq 0:23)
10X-RAY DIFFRACTION10chain 'B' and (resseq 24:82)
11X-RAY DIFFRACTION11chain 'B' and (resseq 83:100)
12X-RAY DIFFRACTION12chain 'B' and (resseq 101:129)
13X-RAY DIFFRACTION13chain 'B' and (resseq 130:152)
14X-RAY DIFFRACTION14chain 'B' and (resseq 153:214)
15X-RAY DIFFRACTION15chain 'B' and (resseq 215:222)
16X-RAY DIFFRACTION16chain 'B' and (resseq 223:242)
17X-RAY DIFFRACTION17chain 'B' and (resseq 243:256)
18X-RAY DIFFRACTION18chain 'C' and (resseq 0:23)
19X-RAY DIFFRACTION19chain 'C' and (resseq 24:129)
20X-RAY DIFFRACTION20chain 'C' and (resseq 130:152)
21X-RAY DIFFRACTION21chain 'C' and (resseq 153:197)
22X-RAY DIFFRACTION22chain 'C' and (resseq 198:222)
23X-RAY DIFFRACTION23chain 'C' and (resseq 223:253)
24X-RAY DIFFRACTION24chain 'C' and (resseq 254:265)
25X-RAY DIFFRACTION25chain 'D' and (resseq 0:23)
26X-RAY DIFFRACTION26chain 'D' and (resseq 24:82)
27X-RAY DIFFRACTION27chain 'D' and (resseq 83:100)
28X-RAY DIFFRACTION28chain 'D' and (resseq 101:129)
29X-RAY DIFFRACTION29chain 'D' and (resseq 130:152)
30X-RAY DIFFRACTION30chain 'D' and (resseq 153:175)
31X-RAY DIFFRACTION31chain 'D' and (resseq 176:197)
32X-RAY DIFFRACTION32chain 'D' and (resseq 198:214)
33X-RAY DIFFRACTION33chain 'D' and (resseq 215:222)
34X-RAY DIFFRACTION34chain 'D' and (resseq 223:243)
35X-RAY DIFFRACTION35chain 'D' and (resseq 244:256)
36X-RAY DIFFRACTION36chain 'E' and (resseq 0:69)
37X-RAY DIFFRACTION37chain 'E' and (resseq 70:129)
38X-RAY DIFFRACTION38chain 'E' and (resseq 130:152)
39X-RAY DIFFRACTION39chain 'E' and (resseq 153:214)
40X-RAY DIFFRACTION40chain 'E' and (resseq 215:222)
41X-RAY DIFFRACTION41chain 'E' and (resseq 223:242)
42X-RAY DIFFRACTION42chain 'E' and (resseq 243:256)

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