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- PDB-4qtn: Crystal structure of the Vitamin B3 transporter PnuC -

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Basic information

Entry
Database: PDB / ID: 4qtn
TitleCrystal structure of the Vitamin B3 transporter PnuC
ComponentsNicotinamide riboside transporter PnuC
KeywordsTRANSPORT PROTEIN / membrane transport / vitamin transport / Nicotinamide riboside uptake
Function / homologyNicotinamide mononucleotide transporter PnuC / Nicotinamide mononucleotide transporter / nicotinamide riboside transmembrane transporter activity / protein homotrimerization / membrane => GO:0016020 / identical protein binding / plasma membrane / Nicotinamide riboside / Nicotinamide riboside transporter PnuC
Function and homology information
Biological speciesNeisseria mucosa ATCC 25996 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsGuskov, A. / Jaehme, M. / Slotboom, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Crystal structure of the Vitamin B3 transporter PnuC
Authors: Jaehme, M. / Guskov, A. / Slotboom, D.J.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide riboside transporter PnuC
B: Nicotinamide riboside transporter PnuC
C: Nicotinamide riboside transporter PnuC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,67310
Polymers84,7383
Non-polymers1,9357
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-59 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.320, 112.930, 120.370
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
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 236
2010B2 - 236
1020A2 - 235
2020C2 - 235
1030B2 - 235
2030C2 - 235

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Nicotinamide riboside transporter PnuC


Mass: 28245.893 Da / Num. of mol.: 3 / Fragment: UNP residues 28-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria mucosa ATCC 25996 (bacteria) / Gene: pnuC, NEIMUCOT_05996 / Production host: Escherichia coli (E. coli) / References: UniProt: D2ZZC1
#2: Chemical ChemComp-NNR / Nicotinamide riboside / 3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium


Mass: 255.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N2O5
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG3350, 0.1 M Succinic Acid, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794, 0.9800, 0.972
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.981
30.9721
ReflectionResolution: 2.8→50 Å / Num. all: 31993 / Num. obs: 31933 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / Num. unique all: 3134 / % possible all: 100

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Processing

Software
NameVersionClassification
DA+data collection
PHENIXmodel building
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→48.31 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.913 / SU B: 55.299 / SU ML: 0.438 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27582 1597 5 %RANDOM
Rwork0.24392 ---
all0.24554 31993 --
obs0.24554 30336 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--4.37 Å20 Å2
3----4.52 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 134 0 5808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9648169
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60822.57214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.42615869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6261518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024281
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9836.1032825
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.3789.1483526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7696.43157
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.53459.02226163
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3100.15
12B3100.15
21A3090.12
22C3090.12
31B3090.16
32C3090.16
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 116 -
Rwork0.46 2211 -
obs--100 %
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)
14.86260.5439-2.06070.20020.69797.92550.40590.62150.3981-0.00210.0247-0.0272-0.1098-0.2587-0.43060.22560.16960.08660.55950.16670.493456.292981.719743.6112
221.34714.7886-10.384211.8508-5.73756.4138-0.53160.7533-1.2197-0.11740.1549-0.89320.4919-0.64880.37670.93790.08950.00361.01970.02310.874160.716374.063223.947
31.00621.5759-1.70583.1771-0.396910.7451-0.15740.31890.2013-0.55050.3830.4026-0.4938-0.3174-0.22560.21890.2349-0.05930.92310.03920.37250.376775.153641.4376
413.2403-11.65155.446713.7525-4.73642.2436-0.00461.1528-1.2432-0.21150.49531.21180.02360.4971-0.49080.7805-0.10390.01710.8303-0.07080.462248.786267.50429.4165
515.84611.8047-13.15668.805-9.81310.9447-0.7402-0.7853-1.7709-0.5378-0.626-1.22810.56860.59061.36621.1986-0.08560.02911.7217-0.10610.997252.581658.342426.9985
67.54422.31841.37452.4349-1.6783.06640.28840.53470.0457-0.44160.27930.83890.941-0.0313-0.56770.4286-0.01430.1541.1467-0.06541.042840.064469.532142.5881
730.284534.05078.221148.071611.76492.8957-0.2010.08090.3071-0.10530.336-0.2953-0.10570.0865-0.1350.6320.16060.11020.679-0.02510.520747.941182.524756.5346
83.4828-0.38020.288516.68534.04877.5921-0.21740.2737-0.76670.26070.40010.39951.0783-0.1215-0.18270.1917-0.0928-0.03920.6570.04260.574542.835754.396954.2103
911.2782-1.54434.93784.99297.198515.16710.83521.6271-1.0017-0.1926-0.1396-0.10740.25150.7327-0.69561.0401-0.0532-0.18691.3023-0.09851.077541.251647.426831.6212
1011.0941-2.7873-2.00545.7872.37827.00150.12570.9158-0.5468-0.8308-0.37940.49930.4282-0.23830.25370.2543-0.0637-0.13830.4870.0080.405349.71659.340745.1247
1119.55770.4459-19.82931.61447.393958.57890.50841.0911-0.9506-0.1840.3814-0.4333-1.38140.9123-0.88981.03450.1540.20760.94370.1180.850362.480956.636227.0847
128.1734-0.9919-5.28463.86661.719711.27310.43970.43760.1776-0.3993-0.12070.0371-1.0316-0.2933-0.31910.15670.026-0.09290.30120.04780.411255.69568.672548.2978
1326.208713.1645-12.772710.2978-6.87256.30320.6184-0.35841.23240.1531-0.17-0.4887-0.34660.2605-0.44840.3581-0.0894-0.09430.7337-0.02090.569393.058170.195561.107
1412.9416-0.4771-5.70943.2202-3.33576.4662-0.77340.742-1.3617-0.68970.32130.24451.1855-0.65120.45210.36990.09440.03930.5761-0.08840.475282.51158.705755.1272
159.04174.1869-0.70637.4607-6.53227.046-0.18111.2534-1.0275-1.3744-0.101-0.63271.44950.7560.28210.5590.23270.11620.8551-0.0720.576390.059954.785642.5351
165.0339.3219-1.005217.5039-1.74093.7569-0.39720.2095-0.2358-0.82690.1642-0.606-0.14470.98410.2330.07570.01490.06130.64750.09140.525887.151872.245652.1511
174.8773.36744.24510.3322.42523.85980.16340.011-0.29880.51040.01930.41330.35870.2061-0.18270.43130.14170.32681.0183-0.06560.429690.802767.249739.4751
181.767-1.50331.393237.5006-12.91044.8972-0.15170.65880.8202-1.3243-0.1440.46090.33770.33530.29570.76870.22350.06461.0187-0.00420.715184.474463.211128.9141
199.9557-0.7559-1.04443.0585-4.43047.0130.11920.7650.2128-0.1645-0.06850.1269-0.0230.0048-0.05060.7388-0.0036-0.06180.71670.14620.657888.317477.412140.0154
2014.073-2.325911.9142.4402-1.757313.1485-0.0194-0.00120.2557-0.10390.106-0.1422-0.0493-0.0116-0.08660.187-0.06860.10760.42680.0220.477677.921283.453752.5766
2111.2971-1.0904-3.5759.231511.842915.78590.90141.7753-1.1446-3.0157-0.3697-0.4807-3.7807-0.5223-0.53171.42550.37750.0411.76660.04650.725277.160779.677723.3485
226.49412.34381.458611.54872.5570.7356-0.10040.9381-0.0156-0.84150.0953-0.1453-0.17240.28160.00520.10190.02160.04570.75290.13470.348475.481775.091540.6209
2312.31250.68511.080816.870411.74912.7202-0.44720.8706-2.6252-1.30110.3229-0.14411.04110.71650.12431.00440.10470.16480.8923-0.15220.814576.676456.567331.1018
244.9410.4873-1.007914.19765.89969.4316-0.00660.12340.16810.56330.1279-0.01520.63160.4558-0.12130.04840.039-0.03430.42310.04330.321477.18769.851752.0142
255.4393-0.5502-1.33226.4292.11728.2610.15810.2929-0.7499-0.3107-0.12950.49451.28840.1045-0.02860.3455-0.0937-0.09890.528-0.06020.684553.039245.318957.3873
263.51960.0801-2.1581.2417-1.86448.25960.1489-0.1183-1.3482-0.1273-0.17480.37591.2211-0.5930.0260.5181-0.0523-0.19280.3853-0.01410.682861.180641.518458.7049
2714.0264-2.1617-8.89850.37062.163630.6765-0.12621.1381-1.45570.0208-0.15370.20622.49450.88520.27980.84580.1435-0.12020.4704-0.16130.755364.827434.794648.9076
2843.336910.09716.147114.5421-1.953221.75120.25420.7263-1.44160.120.2847-1.73560.3710.7955-0.53891.01220.1001-0.06030.6981-0.25670.743270.61836.202940.2894
295.0472-1.86962.81258.754-4.58612.9515-0.30321.1144-0.9557-1.1441-0.2461-0.32140.83340.20290.54920.62330.0566-0.11050.5827-0.07350.975372.262234.660357.2756
3026.0927-9.722-6.085512.93512.548513.28820.32230.2018-0.51120.1494-0.25510.28880.067-0.0394-0.06720.563-0.1405-0.07470.47260.07190.50164.209845.043274.1942
3124.0124.2288-12.47656.1653-3.63387.7510.4223-0.85360.10060.1792-0.2011-0.42960.27640.6091-0.22110.32340.1168-0.16560.4138-0.01450.372682.901152.020165.667
3210.131612.985511.526934.261312.061913.61150.30690.6871-0.8023-2.10390.1241-2.47490.73920.7074-0.4310.6930.17170.171.0646-0.3611.156288.311539.480749.4583
3317.1463-3.3492-9.958810.53688.3579.97361.2821-0.56231.3993-1.1023-0.3229-0.6298-1.2026-0.0709-0.95931.39150.0798-0.0691.0832-0.08591.300886.157433.472640.8751
345.6922-0.0406-0.61683.8818-4.12989.6044-0.13910.2903-0.5731-0.6158-0.401-0.07891.31620.33010.54020.27440.1718-0.06030.4003-0.0810.435475.650447.566254.4622
3511.8371-7.72050.01775.20290.27722.02020.76072.5190.5687-0.7023-1.6583-0.00691.3327-0.35540.89762.1745-0.1399-0.1331.5434-0.34471.017367.726944.375133.9415
365.62740.93482.58125.60424.011413.57390.14950.1741-0.1510.1215-0.37230.52031.0176-0.50050.22280.1390.0483-0.05540.3210.03940.399965.698651.996757.9421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 35
2X-RAY DIFFRACTION2A36 - 42
3X-RAY DIFFRACTION3A43 - 68
4X-RAY DIFFRACTION4A69 - 80
5X-RAY DIFFRACTION5A81 - 87
6X-RAY DIFFRACTION6A88 - 112
7X-RAY DIFFRACTION7A113 - 121
8X-RAY DIFFRACTION8A122 - 144
9X-RAY DIFFRACTION9A145 - 156
10X-RAY DIFFRACTION10A157 - 195
11X-RAY DIFFRACTION11A196 - 205
12X-RAY DIFFRACTION12A206 - 236
13X-RAY DIFFRACTION13B2 - 17
14X-RAY DIFFRACTION14B18 - 31
15X-RAY DIFFRACTION15B32 - 51
16X-RAY DIFFRACTION16B52 - 66
17X-RAY DIFFRACTION17B67 - 77
18X-RAY DIFFRACTION18B78 - 87
19X-RAY DIFFRACTION19B88 - 106
20X-RAY DIFFRACTION20B107 - 139
21X-RAY DIFFRACTION21B140 - 154
22X-RAY DIFFRACTION22B155 - 192
23X-RAY DIFFRACTION23B193 - 206
24X-RAY DIFFRACTION24B207 - 236
25X-RAY DIFFRACTION25C2 - 41
26X-RAY DIFFRACTION26C42 - 69
27X-RAY DIFFRACTION27C70 - 78
28X-RAY DIFFRACTION28C79 - 87
29X-RAY DIFFRACTION29C88 - 104
30X-RAY DIFFRACTION30C105 - 120
31X-RAY DIFFRACTION31C121 - 137
32X-RAY DIFFRACTION32C138 - 149
33X-RAY DIFFRACTION33C150 - 156
34X-RAY DIFFRACTION34C157 - 195
35X-RAY DIFFRACTION35C196 - 205
36X-RAY DIFFRACTION36C206 - 236

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