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- PDB-4f35: Crystal Structure of a bacterial dicarboxylate/sodium symporter -

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Basic information

Entry
Database: PDB / ID: 4f35
TitleCrystal Structure of a bacterial dicarboxylate/sodium symporter
ComponentsTransporter, NadC family
KeywordsTRANSPORT PROTEIN / TRANSPORTER
Function / homology
Function and homology information


citrate transmembrane transporter activity / succinate transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Citrate transporter-like domain / Citrate transporter / Sodium:sulfate symporter transmembrane region / Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Solute carrier family 13
Similarity search - Domain/homology
CITRIC ACID / Transporter, NadC family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.196 Å
AuthorsMancusso, R.L. / Gregorio, G.G. / Liu, Q. / Wang, D.N.
CitationJournal: Nature / Year: 2012
Title: Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter.
Authors: Mancusso, R. / Gregorio, G.G. / Liu, Q. / Wang, D.N.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Transporter, NadC family
B: Transporter, NadC family
A: Transporter, NadC family
C: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,53114
Polymers196,9444
Non-polymers1,58810
Water905
1
D: Transporter, NadC family
C: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3237
Polymers98,4722
Non-polymers8515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-64 kcal/mol
Surface area32560 Å2
MethodPISA
2
B: Transporter, NadC family
A: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2087
Polymers98,4722
Non-polymers7375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-61 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.330, 100.870, 164.568
Angle α, β, γ (deg.)90.00, 101.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transporter, NadC family


Mass: 49235.930 Da / Num. of mol.: 4 / Fragment: UNP residues 14-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KNE0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 29% PEG 1000, 0.05M Lithium citrate, 0.05M MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.196→44.52 Å / Num. obs: 54103 / % possible obs: 97.9 % / Observed criterion σ(F): 1.51 / Observed criterion σ(I): 1.51
Reflection shellResolution: 3.196→3.27 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.196→44.377 Å / SU ML: 1.06 / σ(F): 1.35 / Phase error: 33.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2913 2024 3.88 %
Rwork0.228 --
obs0.2304 52199 96.53 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 90.681 Å2 / ksol: 0.279 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2923 Å2-0 Å219.3573 Å2
2---8.057 Å2-0 Å2
3---3.7646 Å2
Refinement stepCycle: LAST / Resolution: 3.196→44.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12279 0 106 5 12390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112645
X-RAY DIFFRACTIONf_angle_d1.55717297
X-RAY DIFFRACTIONf_dihedral_angle_d17.6664050
X-RAY DIFFRACTIONf_chiral_restr0.0932218
X-RAY DIFFRACTIONf_plane_restr0.0072090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.196-3.27590.4074980.35812647X-RAY DIFFRACTION71
3.2759-3.36440.40751470.32833642X-RAY DIFFRACTION99
3.3644-3.46340.3771490.30843688X-RAY DIFFRACTION100
3.4634-3.57510.36851490.27533683X-RAY DIFFRACTION100
3.5751-3.70280.36211490.26153655X-RAY DIFFRACTION100
3.7028-3.8510.34121490.24273697X-RAY DIFFRACTION100
3.851-4.02620.30091490.22583694X-RAY DIFFRACTION100
4.0262-4.23830.29171490.21073697X-RAY DIFFRACTION100
4.2383-4.50360.25621500.19783690X-RAY DIFFRACTION100
4.5036-4.85090.24671500.1753732X-RAY DIFFRACTION100
4.8509-5.33830.23671490.17633709X-RAY DIFFRACTION100
5.3383-6.10910.36421490.21963698X-RAY DIFFRACTION100
6.1091-7.69030.24871510.21623749X-RAY DIFFRACTION100
7.6903-44.38130.25961360.24643194X-RAY DIFFRACTION84
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)
17.71431.77891.9183.437-0.38494.8292-0.17220.8776-0.0093-0.65790.52610.2032-0.4834-0.2638-0.30830.77020.07340.20990.45510.18780.78439.445660.3718-0.3402
21.06940.56750.10551.78730.23381.16760.3588-0.03390.2098-0.0514-0.0776-0.1336-0.44620.0573-0.10380.5061-0.04090.14060.3603-0.04550.525835.344745.482614.2111
31.37230.32230.74312.1414-0.90041.0340.0358-0.8170.81611.86560.71391.0261-0.8861-0.3874-0.25381.4325-0.21540.46790.8786-0.29570.893225.446355.114545.996
40.1806-0.4523-0.07993.31131.54651.7585-0.3362-0.45470.05910.73210.24290.4002-0.1432-0.2059-0.06711.2819-0.05940.29370.7795-0.32951.009522.002960.26338.1919
53.4667-0.1005-0.45490.86610.43614.7491-0.3522-0.44490.08330.66520.05820.42460.46230.06560.06440.9244-0.11760.25980.5853-0.10420.621937.662954.572229.1196
68.9016-7.7527-3.0379.62184.41825.36910.2682-0.50010.85620.3832-0.35320.29890.24840.715-0.01241.0926-0.28080.17230.7427-0.30490.82341.433359.052837.0618
70.82170.32060.09982.8081-0.14940.73140.2557-0.36730.0350.6798-0.23210.0439-0.20390.2718-0.03420.7879-0.02990.16020.46430.02210.514638.053538.372936.184
81.43630.1179-1.06192.4182-0.23813.5559-0.2930.15890.13590.38720.09010.33660.509-0.38660.10720.6535-0.00030.2850.4262-0.07070.559633.68843.262418.8067
90.83140.2796-1.27092.29211.69464.26010.2255-0.35150.3625-0.30640.2489-0.3327-0.89390.8483-0.30550.8132-0.11010.2660.5029-0.13210.780648.698662.573717.8708
105.05673.50451.50964.9448-2.65346.0112-0.36620.62982.0672-1.1009-0.2996-0.1315-2.255-0.0698-0.09731.24390.80180.8722-3.5294-1.65561.494125.370166.345727.8194
112.0816-6.80610.56068.3241-1.56923.15330.5938-0.15610.42330.5463-0.0560.1621-1.69870.5556-0.39971.6331-0.32150.32530.7843-0.03880.936942.644368.647931.099
123.03481.7586-2.46925.6569-2.9856.7368-0.55780.7374-0.0975-0.55330.3510.45481.2453-1.08480.08671.4383-0.22440.31440.5273-0.07970.6332-11.5905-7.100250.8604
130.6176-1.2415-0.50754.45370.94731.9948-0.19070.0869-0.6931-1.0679-0.1145-0.19940.5074-0.30370.21881.2552-0.18390.39270.4669-0.08740.7964-9.19575.68157.0064
142.7784-3.2849-0.16544.27330.91492.33340.67420.17570.6647-0.1865-0.585-1.68860.07381.11080.06250.9240.23290.22550.93390.42841.459820.255613.377669.0713
158.1959-0.6353-1.42244.7006-0.34875.81461.50910.47990.57980.6297-1.1038-0.0318-0.81350.1694-0.48321.19390.12250.48010.89420.03221.601126.37156.633261.7488
160.61680.0018-0.15232.32410.6651.0906-0.3941-0.578-0.74870.63160.1328-0.78020.56280.68490.18790.97260.25220.0840.85540.17250.990112.39758.172274.8956
175.89063.3721-0.01417.6248-0.11643.73440.1866-0.51050.8550.4538-0.6160.15410.31350.25860.13630.77470.030.18060.499-0.01990.68440.813413.103462.9397
181.23260.1030.53191.63750.38670.3866-0.2340.053-0.3637-0.03220.0196-0.49420.5220.23360.11841.11180.2440.41220.54840.11220.91495.8523-9.444767.2423
191.0061-0.0669-1.20643.33831.56092.40840.15150.02960.25581.0943-0.0202-0.00120.0784-0.1798-0.13320.8141-0.02980.16510.42860.03670.7504-4.968232.575374.9756
200.5730.40350.01061.160.08071.4032-0.00270.77440.4318-0.88490.4067-0.1078-0.3279-0.3208-0.22841.1353-0.02450.23680.78590.21210.6664-5.888633.631540.3509
210.0786-0.04380.1263.25190.15320.59240.0520.88620.3071-1.52650.36070.0408-0.3770.1638-0.04390.7745-0.27570.16810.82370.10180.4968-7.255222.820435.4798
227.71930.13970.77916.2915-2.51916.8147-0.66940.7354-1.242-0.5048-0.1530.70450.7052-0.60490.74610.8122-0.18930.20440.6153-0.11880.7918-17.258312.626947.6804
231.6974-0.24770.03832.0431-0.1752.5069-0.48120.3083-0.3821-0.046-0.2367-0.17541.06730.17470.38380.90980.00480.28530.54550.10050.4785-4.17621.260357.7061
240.35940.4417-0.76341.2119-1.72934.42490.3670.13780.44850.21040.11660.4034-1.1077-0.4695-0.30541.01970.08520.48350.52660.11250.9945-18.208241.051663.0831
251.9491-0.57271.27282.9152-0.24553.3027-0.7208-0.74140.7976-1.0531-1.2491.3299-2.4705-1.9946-0.17091.5455-0.42691.3595-0.40561.13090.23-7.128146.807848.2886
265.7322-0.3583-1.77664.3686-1.93188.5289-0.1213-0.87420.08370.29920.2004-0.33050.64260.73190.10041.16810.14840.16840.55010.07840.472837.182714.772427.2878
270.8149-0.21370.01891.6775-0.15052.2272-0.00660.0812-0.14270.1449-0.08610.55220.0963-0.38610.10480.71730.04390.25860.4335-0.02780.666224.878532.772111.7491
285.4667-0.61961.18274.8238-1.27741.8921-0.47660.720.4017-0.65750.0596-0.1602-0.0914-0.49180.45790.587-0.0650.10790.91340.02460.62736.580730.31453.7312
291.01821.07531.36173.929-0.86783.56470.1731-1.1134-0.20440.8545-0.17061.4821-0.3124-0.5201-0.17090.7049-0.23650.26630.8394-0.14470.99850.166322.80187.4554
302.03820.6161-0.87611.02520.2172.2214-0.26870.5238-0.1192-0.42990.17680.00470.3067-0.42710.00380.6007-0.00040.13210.5211-0.01240.426624.33732.39631.4338
319.610.13676.28460.0365-0.04314.5790.68260.6332-1.7995-0.3507-0.2248-1.08342.0682-0.0071-0.52421.5932-0.07170.58790.4638-0.02481.2736.45134.66336.1675
322.55841.06431.22122.3166-0.00820.6235-0.4089-0.2238-0.72310.7145-0.31550.27371.1162-0.33250.15010.4857-0.19120.20030.3718-0.07870.524326.345715.568412.4085
331.25930.97760.10552.1273-0.72111.1785-0.71580.0834-1.07730.13970.04280.23790.5915-0.3160.37130.791-0.2940.21930.564-0.16630.536518.810817.55039.4505
342.4093-0.1766-7.38786.2347-2.22868.4714-0.1868-0.6738-0.0917-1.01890.171-0.69140.47120.3739-0.00911.0441-0.36560.13071.0518-0.26950.684716.901610.8031.8187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resseq 19:59)
2X-RAY DIFFRACTION2chain 'D' and (resseq 60:113)
3X-RAY DIFFRACTION3chain 'D' and (resseq 114:146)
4X-RAY DIFFRACTION4chain 'D' and (resseq 147:181)
5X-RAY DIFFRACTION5chain 'D' and (resseq 182:213)
6X-RAY DIFFRACTION6chain 'D' and (resseq 214:237)
7X-RAY DIFFRACTION7chain 'D' and (resseq 238:305)
8X-RAY DIFFRACTION8chain 'D' and (resseq 306:339)
9X-RAY DIFFRACTION9chain 'D' and (resseq 340:412)
10X-RAY DIFFRACTION10chain 'D' and (resseq 413:435)
11X-RAY DIFFRACTION11chain 'D' and (resseq 436:462)
12X-RAY DIFFRACTION12chain 'B' and (resseq 19:58)
13X-RAY DIFFRACTION13chain 'B' and (resseq 59:94)
14X-RAY DIFFRACTION14chain 'B' and (resseq 95:146)
15X-RAY DIFFRACTION15chain 'B' and (resseq 147:179)
16X-RAY DIFFRACTION16chain 'B' and (resseq 180:305)
17X-RAY DIFFRACTION17chain 'B' and (resseq 306:338)
18X-RAY DIFFRACTION18chain 'B' and (resseq 339:462)
19X-RAY DIFFRACTION19chain 'A' and (resseq 19:94)
20X-RAY DIFFRACTION20chain 'A' and (resseq 95:237)
21X-RAY DIFFRACTION21chain 'A' and (resseq 238:276)
22X-RAY DIFFRACTION22chain 'A' and (resseq 277:305)
23X-RAY DIFFRACTION23chain 'A' and (resseq 306:338)
24X-RAY DIFFRACTION24chain 'A' and (resseq 339:412)
25X-RAY DIFFRACTION25chain 'A' and (resseq 413:462)
26X-RAY DIFFRACTION26chain 'C' and (resseq 18:59)
27X-RAY DIFFRACTION27chain 'C' and (resseq 60:131)
28X-RAY DIFFRACTION28chain 'C' and (resseq 132:164)
29X-RAY DIFFRACTION29chain 'C' and (resseq 165:193)
30X-RAY DIFFRACTION30chain 'C' and (resseq 194:339)
31X-RAY DIFFRACTION31chain 'C' and (resseq 340:365)
32X-RAY DIFFRACTION32chain 'C' and (resseq 366:392)
33X-RAY DIFFRACTION33chain 'C' and (resseq 393:436)
34X-RAY DIFFRACTION34chain 'C' and (resseq 437:462)

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