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- PDB-7tak: Structure of a NAT transporter -

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Basic information

Entry
Database: PDB / ID: 7tak
TitleStructure of a NAT transporter
ComponentsPutative membrane protein PurT
KeywordsTRANSPORT PROTEIN / nucleobase ascorbic acid transporter
Function / homologynucleobase transmembrane transporter activity / Nucleobase cation symporter 2 family / Permease family / membrane / GUANINE / Putative membrane protein
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79828 Å
AuthorsWeng, J. / Zhou, X. / Ren, Z. / Chen, K. / Zhou, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM119396 United States
CitationJournal: To Be Published
Title: Structure of a NAT transporter
Authors: Weng, J. / Zhou, X. / Ren, Z. / Chen, K. / Zhou, M.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _struct_keywords.text
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative membrane protein PurT
B: Putative membrane protein PurT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8724
Polymers103,5702
Non-polymers3022
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-86 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.713, 135.993, 79.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative membrane protein PurT


Mass: 51785.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Gene: CPS_4258 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47WB4
#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 277.15 K / Method: evaporation
Details: 30% (v/v) PEG 400, 0.1 M MES pH 6.0, 3 mM Na-glycochenodeoxycholate and 0.5 mM 6-bromopurine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.915 Å
DetectorType: MPCCD / Detector: CCD / Date: Jan 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.79828→48.0306 Å / Num. obs: 35338 / % possible obs: 98.7018 % / Redundancy: 5 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 5
Reflection shellResolution: 2.7983→2.8983 Å / Rmerge(I) obs: 0.25 / Num. unique obs: 2307

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xls

5xls


Resolution: 2.79828→41.781 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1771 5.01 %
Rwork0.198 --
obs0.1997 35338 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79828→41.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6992 0 22 17 7031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087216
X-RAY DIFFRACTIONf_angle_d1.1929836
X-RAY DIFFRACTIONf_dihedral_angle_d12.3792564
X-RAY DIFFRACTIONf_chiral_restr0.0541127
X-RAY DIFFRACTIONf_plane_restr0.0071213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7983-2.87390.3341030.33822307X-RAY DIFFRACTION90
2.8739-2.95850.34311180.30892499X-RAY DIFFRACTION96
2.9585-3.05390.28851420.27262541X-RAY DIFFRACTION99
3.0539-3.1630.3241200.25122613X-RAY DIFFRACTION100
3.163-3.28960.25651370.22272574X-RAY DIFFRACTION100
3.2896-3.43930.22851450.19792575X-RAY DIFFRACTION100
3.4393-3.62050.27221460.1872573X-RAY DIFFRACTION100
3.6205-3.84720.22321590.17822575X-RAY DIFFRACTION100
3.8472-4.1440.21761380.1642625X-RAY DIFFRACTION100
4.144-4.56060.18711550.15732598X-RAY DIFFRACTION100
4.5606-5.21940.22941410.17542639X-RAY DIFFRACTION100
5.2194-6.57180.27231250.23572692X-RAY DIFFRACTION100
6.5718-41.780.211420.19482756X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.22370.3288-0.12122.87050.26771.71640.016-0.05250.7020.16280.0444-0.8120.13430.1301-0.0320.68330.0081-0.09090.9178-0.05390.866438.5722.9321.98
25.3760.6729-0.39745.732-1.40689.1798-0.38340.2997-0.6725-0.17630.0857-0.76220.09820.10170.250.60890.0475-0.0830.765-0.12210.96234.221-13.52314.466
35.109-1.7376-0.49854.6917-0.27622.2175-0.0632-0.00980.28970.16070.1883-1.0607-0.11970.3558-0.09230.6283-0.0648-0.06241.013-0.04860.870836.9970.18919.719
43.74150.4062-0.74613.0959-0.34590.7529-0.0441-0.9694-1.16190.59420.2577-0.30.19890.0684-0.25690.88850.0891-0.24581.16020.13511.014825.765-18.46226.292
54.8554-0.4224-1.19294.74511.89683.08070.06840.3059-1.59430.2316-0.00310.77310.1961-0.1958-0.08130.633-0.0153-0.13770.8909-0.04041.1761-0.982-32.01817.009
64.6468-0.34530.33732.4229-0.40763.1301-0.0998-0.7444-1.13540.41680.3464-0.38190.1431-0.0613-0.16430.9963-0.0198-0.05770.97840.30741.022411.611-27.81828.228
76.02980.1919-1.83341.9725-0.65682.80090.11810.489-1.5818-0.2698-0.0434-0.14850.28050.0298-0.10340.83360.0372-0.05040.7268-0.14981.031410.039-28.38614.356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:130 )A1 - 130
2X-RAY DIFFRACTION2( CHAIN A AND RESID 131:207 )A131 - 207
3X-RAY DIFFRACTION3( CHAIN A AND RESID 208:366 )A208 - 366
4X-RAY DIFFRACTION4( CHAIN A AND RESID 367:457 )A367 - 457
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:130 )B2 - 130
6X-RAY DIFFRACTION6( CHAIN B AND RESID 131:233 )B131 - 233
7X-RAY DIFFRACTION7( CHAIN B AND RESID 234:457 )B234 - 457

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