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- PDB-3tds: Crystal structure of HSC F194I -

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Basic information

Entry
Database: PDB / ID: 3tds
TitleCrystal structure of HSC F194I
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: 1.975 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 1.4Feb 28, 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
E: formate/nitrite transporter
A: formate/nitrite transporter
B: formate/nitrite transporter
C: formate/nitrite transporter
D: formate/nitrite transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,40614
Polymers141,1675
Non-polymers2,2399
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20680 Å2
ΔGint-142 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.611, 118.051, 150.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21A
31B
41C
51D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain E and (resseq 5:220 or resseq 225:259 ) and (not element H)E5 - 220
121chain E and (resseq 5:220 or resseq 225:259 ) and (not element H)E225 - 259
211chain A and (resseq 5:220 or resseq 225:259 ) and (not element H)A5 - 220
221chain A and (resseq 5:220 or resseq 225:259 ) and (not element H)A225 - 259
311chain B and (resseq 5:220 or resseq 225:259 ) and (not element H)B5 - 220
321chain B and (resseq 5:220 or resseq 225:259 ) and (not element H)B225 - 259
411chain C and (resseq 5:220 or resseq 225:259 ) and (not element H)C5 - 220
421chain C and (resseq 5:220 or resseq 225:259 ) and (not element H)C225 - 259
511chain D and (resseq 5:220 or resseq 225:259 ) and (not element H)D5 - 220
521chain D and (resseq 5:220 or resseq 225:259 ) and (not element H)D225 - 259

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Components

#1: Protein
formate/nitrite transporter


Mass: 28233.426 Da / Num. of mol.: 5 / Mutation: F194I
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.: 4 / 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.: 5
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.: 304 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 400, pH 7.5, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.975→50 Å / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.03-2.077.50.7711100
2.07-2.17.50.6441100
2.1-2.147.50.5481100
2.14-2.197.50.4441100
2.19-2.237.50.3811100
2.23-2.297.50.3151100
2.29-2.347.50.281100
2.34-2.417.50.2381100
2.41-2.487.50.2111100
2.48-2.567.50.191100
2.56-2.657.50.1681100
2.65-2.767.50.1481100
2.76-2.887.40.1271100
2.88-3.037.40.1111100
3.03-3.227.40.094199.9
3.22-3.477.30.0881100
3.47-3.826.80.078199.9
3.82-4.376.60.066199.6
4.37-5.516.60.059199.1
5.51-506.50.052194.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.975→41.974 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / σ(F): 1.33 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 6085 5.03 %
Rwork0.1768 --
obs0.1782 121087 98.43 %
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.343 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.4537 Å20 Å20 Å2
2--10.5016 Å2-0 Å2
3---14.9483 Å2
Refinement stepCycle: LAST / Resolution: 1.975→41.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9543 0 152 304 9999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079847
X-RAY DIFFRACTIONf_angle_d0.89913316
X-RAY DIFFRACTIONf_dihedral_angle_d13.9983408
X-RAY DIFFRACTIONf_chiral_restr0.0611690
X-RAY DIFFRACTIONf_plane_restr0.0031576
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11E1850X-RAY DIFFRACTIONPOSITIONAL0.045
12A1850X-RAY DIFFRACTIONPOSITIONAL0.045
13B1854X-RAY DIFFRACTIONPOSITIONAL0.054
14C1854X-RAY DIFFRACTIONPOSITIONAL0.077
15D1854X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9752-2.04580.25775870.226710046X-RAY DIFFRACTION87
2.0458-2.12770.24846020.211911527X-RAY DIFFRACTION100
2.1277-2.22450.22436230.187911573X-RAY DIFFRACTION100
2.2245-2.34180.20816140.166511582X-RAY DIFFRACTION100
2.3418-2.48850.19276200.158311596X-RAY DIFFRACTION100
2.4885-2.68060.20925920.160711680X-RAY DIFFRACTION100
2.6806-2.95030.19916030.167711683X-RAY DIFFRACTION100
2.9503-3.3770.215990.176911714X-RAY DIFFRACTION100
3.377-4.25410.19336110.166111778X-RAY DIFFRACTION100
4.2541-41.98350.20336340.187211823X-RAY DIFFRACTION97
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)
12.643-1.91291.73265.8729-5.84087.105-0.00720.04230.0605-0.0863-0.1468-1.59060.04760.41970.25810.2596-0.0277-0.0680.419-0.17190.63942.744748.795928.4929
23.05661.3965-0.28114.3454-0.47771.92180.1189-0.29470.35740.3396-0.01570.1544-0.0684-0.0296-0.07710.22350.02320.02210.2229-0.09290.22517.693348.573826.2305
32.4213-1.0672-1.33453.751-0.7961.32120.0204-0.0440.57010.757-0.2518-0.62230.00490.17730.1390.4864-0.0437-0.16840.4127-0.15950.607539.324550.372135.853
45.5888-0.13091.69692.37110.37082.2620.1335-0.16810.64530.2368-0.0425-0.1712-0.05430.1724-0.00890.3242-0.02090.04420.2828-0.18760.479225.824960.135329.7741
53.3660.53482.70993.6089-0.288.13350.2101-0.78570.34750.532-0.04570.6631-0.124-0.76730.0230.37260.00070.17770.385-0.16760.51195.647654.629634.2454
60.99140.36940.51763.29730.69212.25480.0933-0.13640.22920.5203-0.0379-0.17590.0166-0.1228-0.07170.2871-0.0386-0.03650.2921-0.08050.277322.788645.121233.6837
71.3853-0.69480.61170.91690.87675.78250.0145-0.13610.12890.12530.12820.0027-0.3191-0.47080.20420.59720.14530.29670.6801-0.22680.98274.591862.567135.4319
86.071-4.7359-4.28873.99523.69194.07210.0581-0.49390.16640.87360.0904-0.12970.43080.052-0.07820.4976-0.1173-0.00130.3845-0.17890.415722.612355.959841.9126
94.16123.26823.13523.24110.41488.55450.0687-0.0571-0.46350.33450.3865-0.9610.05530.7731-0.0670.58940.0558-0.44180.3675-0.10080.706941.919241.022740.9161
102.1116-2.8547-1.53194.22712.99375.1215-0.18190.1384-0.2832-0.7160.3301-1.34930.0250.5165-0.20340.5498-0.0620.23240.4643-0.09120.425426.577425.0223-10.2018
111.17660.43270.04873.0556-0.03251.5551-0.06270.2384-0.1093-0.54290.05280.08940.0005-0.0336-0.02170.2356-0.0333-0.01350.2392-0.06170.206411.074218.2789-0.429
124.5717-2.01142.90933.09590.55393.3861-0.0761-0.3234-0.48720.04830.27951.1192-0.0881-0.7235-0.23080.1932-0.0326-0.03560.3443-0.05160.4803-6.156715.59897.0319
131.62410.8980.86993.65460.94341.1564-0.13370.1986-0.0261-0.50410.0530.4127-0.0599-0.0210.07840.2914-0.0164-0.04420.3019-0.02570.23966.231724.2161-0.6235
146.2626-5.84242.02357.9324-1.52828.7636-0.17281.19080.1062-0.82330.3039-0.4747-0.05670.6138-0.21740.6636-0.14570.13150.3764-0.03720.272620.090836.8724-12.6183
157.62840.78216.05653.94820.47036.2413-0.03510.56810.1249-0.57550.1634-0.42540.32510.9117-0.01370.2857-0.04790.17140.2323-0.03610.380631.887751.70421.6675
163.65321.3954-1.61943.631-0.86484.3493-0.01580.17620.2635-0.26140.08650.3748-0.1513-0.2905-0.1050.2140.0228-0.06550.2046-0.00480.24329.53841.2786.3135
175.467-2.53422.99983.37991.37066.62510.14640.01450.5036-0.4956-0.0839-0.3327-0.58230.2297-0.07370.3416-0.01980.10170.21580.010.370626.377357.69952.837
185.11442.5753-0.0134.60920.10321.6892-0.32650.79250.7516-0.93940.3390.3199-0.2961-0.054-0.00610.47490.0347-0.09650.25480.08560.325111.919550.7374-4.5647
191.86711.7283-0.63711.9470.34652.96150.09360.12370.6882-0.2347-0.3111.9572-0.1206-0.51480.28870.29180.0806-0.13580.4074-0.0240.7433-5.324846.46497.5554
201.6969-0.0420.4282.648-0.1191.5799-0.01370.0860.2612-0.40870.0120.4592-0.1402-0.23810.07020.1750.0268-0.0320.15780.01050.279110.839750.6718.9569
213.38820.861-1.66927.5067-3.0746.45520.30050.20970.4054-0.4145-0.1642-0.7107-0.06180.4658-0.11610.3297-0.04870.10360.2443-0.07530.4931.041260.302912.4753
221.6155-0.3210.90782.37110.83030.99390.0151-0.3412-0.2180.94050.0577-0.5740.3090.145-0.10710.5371-0.0505-0.18140.33430.0810.354728.543226.358737.9475
230.0621-0.1618-0.14350.79630.01450.58670.1102-0.2443-0.37120.53130.0367-0.6160.49860.4534-0.20180.44870.0741-0.72280.32770.08650.448136.341820.824437.9792
240.56230.2210.49231.7141-0.01190.63490.1703-0.4458-0.11451.3703-0.0611-0.62310.42830.1532-0.08380.8132-0.0469-0.2240.35380.04130.158424.248523.988542.0318
251.8509-0.09980.92057.621-1.70071.69470.0776-0.80170.15181.70490.10270.6286-0.3146-0.539-0.01011.3202-0.0389-0.01650.65730.05260.270818.724128.093751.6325
261.17170.2427-0.46480.74760.32882.34120.1319-0.5323-0.30360.8054-0.0188-0.32190.0750.12730.0741.03050.0086-0.3640.43870.16070.471529.0713.30544.5337
277.031-5.61172.71817.825-0.82879.20180.21170.11091.1477-0.31250.09-0.39470.2419-0.7016-0.11010.53960.1076-0.20530.77190.06481.091945.1368-0.999130.7101
287.3263-4.25125.36626.6962-4.79479.3246-0.04660.27150.11720.2702-0.1141-1.2947-0.22750.77710.19260.2560.03320.02370.2695-0.11790.709433.6584.82519.8722
291.2572-0.43790.09213.35410.06432.55170.1631-0.0928-0.18210.5202-0.1084-0.07460.2827-0.10860.0110.2803-0.0659-0.02620.1380.04230.219116.959111.94527.0291
303.04880.85550.05574.103-1.36015.1715-0.32740.135-0.7203-0.05290.1754-0.53950.72360.38090.07280.32550.02310.01650.2916-0.03610.603927.3356-0.41859.5383
312.8770.7951-1.22051.65020.06645.5638-0.0247-0.3215-0.71660.7833-0.0779-0.39060.0950.4239-0.0090.58170.0237-0.09340.26770.12910.500322.8824-1.46226.6305
321.91560.42630.18261.2636-0.51261.86440.2111-0.5057-0.07440.7626-0.23970.3642-0.1622-0.3679-0.36950.7464-0.20640.3380.46610.03290.52623.87325.968533.2624
331.8684-0.19270.91061.69710.73841.82190.09410.0645-0.34090.38310.0307-0.29640.3081-0.039-0.08430.2912-0.01910.00270.20510.02140.32115.42399.380817.8512
344.4086-0.75043.56331.78771.77018.207-0.0422-0.75190.00321.339-0.40520.2572-0.7759-0.38770.13651.2722-0.3667-0.00360.97640.25910.88674.144-0.809138.1799
355.38813.4084-3.94017.1627-4.80925.66640.0173-0.1113-0.68630.593-0.2661-0.1573-0.1563-0.07790.26790.443-0.03320.0370.25330.00850.476411.9336-3.690419.4342
361.304-0.7014-0.59693.9679-2.40158.9682-0.40150.4307-0.4319-0.92640.2606-0.97580.39740.63180.24910.322-0.00240.14310.3619-0.10860.582724.37853.7518-0.0116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resseq 1:23)
2X-RAY DIFFRACTION2chain 'E' and (resseq 24:82)
3X-RAY DIFFRACTION3chain 'E' and (resseq 83:100)
4X-RAY DIFFRACTION4chain 'E' and (resseq 101:129)
5X-RAY DIFFRACTION5chain 'E' and (resseq 130:152)
6X-RAY DIFFRACTION6chain 'E' and (resseq 153:214)
7X-RAY DIFFRACTION7chain 'E' and (resseq 215:222)
8X-RAY DIFFRACTION8chain 'E' and (resseq 223:242)
9X-RAY DIFFRACTION9chain 'E' and (resseq 243:256)
10X-RAY DIFFRACTION10chain 'A' and (resseq 0:23)
11X-RAY DIFFRACTION11chain 'A' and (resseq 24:128)
12X-RAY DIFFRACTION12chain 'A' and (resseq 129:152)
13X-RAY DIFFRACTION13chain 'A' and (resseq 153:242)
14X-RAY DIFFRACTION14chain 'A' and (resseq 243:256)
15X-RAY DIFFRACTION15chain 'B' and (resseq 0:23)
16X-RAY DIFFRACTION16chain 'B' and (resseq 24:82)
17X-RAY DIFFRACTION17chain 'B' and (resseq 83:100)
18X-RAY DIFFRACTION18chain 'B' and (resseq 101:129)
19X-RAY DIFFRACTION19chain 'B' and (resseq 130:152)
20X-RAY DIFFRACTION20chain 'B' and (resseq 153:242)
21X-RAY DIFFRACTION21chain 'B' and (resseq 243:256)
22X-RAY DIFFRACTION22chain 'C' and (resseq 0:69)
23X-RAY DIFFRACTION23chain 'C' and (resseq 70:100)
24X-RAY DIFFRACTION24chain 'C' and (resseq 101:197)
25X-RAY DIFFRACTION25chain 'C' and (resseq 198:222)
26X-RAY DIFFRACTION26chain 'C' and (resseq 223:253)
27X-RAY DIFFRACTION27chain 'C' and (resseq 254:265)
28X-RAY DIFFRACTION28chain 'D' and (resseq 0:23)
29X-RAY DIFFRACTION29chain 'D' and (resseq 24:82)
30X-RAY DIFFRACTION30chain 'D' and (resseq 83:100)
31X-RAY DIFFRACTION31chain 'D' and (resseq 101:129)
32X-RAY DIFFRACTION32chain 'D' and (resseq 130:152)
33X-RAY DIFFRACTION33chain 'D' and (resseq 153:214)
34X-RAY DIFFRACTION34chain 'D' and (resseq 215:222)
35X-RAY DIFFRACTION35chain 'D' and (resseq 223:242)
36X-RAY DIFFRACTION36chain 'D' and (resseq 243:256)

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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