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- PDB-7qsq: Permutated N-terminal lobe of the ribose binding protein from The... -

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Basic information

Entry
Database: PDB / ID: 7qsq
TitlePermutated N-terminal lobe of the ribose binding protein from Thermotoga maritima
ComponentsRibose ABC transporter, periplasmic ribose-binding protein
KeywordsSUGAR BINDING PROTEIN / Solute binding protein / circular permutation / Periplasmic binding proteins / domain swapping
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / carbohydrate binding / TRIETHYLENE GLYCOL / Ribose ABC transporter, periplasmic ribose-binding protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsShanmugaratnam, S. / Michel, F. / Hocker, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)647548European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structures of permuted halves of a modern ribose-binding protein.
Authors: Michel, F. / Shanmugaratnam, S. / Romero-Romero, S. / Hocker, B.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose ABC transporter, periplasmic ribose-binding protein
C: Ribose ABC transporter, periplasmic ribose-binding protein
B: Ribose ABC transporter, periplasmic ribose-binding protein
D: Ribose ABC transporter, periplasmic ribose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,88019
Polymers60,7924
Non-polymers1,08715
Water5,675315
1
A: Ribose ABC transporter, periplasmic ribose-binding protein
C: Ribose ABC transporter, periplasmic ribose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,07711
Polymers30,3962
Non-polymers6819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-52 kcal/mol
Surface area11440 Å2
MethodPISA
2
B: Ribose ABC transporter, periplasmic ribose-binding protein
D: Ribose ABC transporter, periplasmic ribose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8038
Polymers30,3962
Non-polymers4066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-58 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.370, 62.770, 76.260
Angle α, β, γ (deg.)90.000, 102.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Ribose ABC transporter, periplasmic ribose-binding protein


Mass: 15198.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0958 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X053
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 4000, 0.2 M Lithium-sulfate, 0.1 M Tris pH 8.0, 4% 2,2,2-Trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.79→48.96 Å / Num. obs: 47556 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.59 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.047 / Rrim(I) all: 0.094 / Net I/σ(I): 8.58
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.324 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 4346 / CC1/2: 0.413 / CC star: 0.765 / Rpim(I) all: 0.788 / Rrim(I) all: 1.548 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS20210323data reduction
XDS20210323data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FN9

2fn9


Resolution: 1.79→48.96 Å / SU ML: 0.262 / Cross valid method: FREE R-VALUE / Phase error: 25.4483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 2088 4.41 %
Rwork0.1913 45206 -
obs0.1933 47294 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.95 Å2
Refinement stepCycle: LAST / Resolution: 1.79→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 68 315 4299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324212
X-RAY DIFFRACTIONf_angle_d0.57115721
X-RAY DIFFRACTIONf_chiral_restr0.0489647
X-RAY DIFFRACTIONf_plane_restr0.0049743
X-RAY DIFFRACTIONf_dihedral_angle_d5.6079615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.40041110.39452404X-RAY DIFFRACTION78.69
1.83-1.880.36321400.32563044X-RAY DIFFRACTION99.28
1.88-1.930.3231410.26973039X-RAY DIFFRACTION99.53
1.93-1.980.28921410.25443058X-RAY DIFFRACTION99.16
1.98-2.050.32831390.25623021X-RAY DIFFRACTION98.14
2.05-2.120.28351400.22193032X-RAY DIFFRACTION99.44
2.12-2.210.25971410.20333049X-RAY DIFFRACTION99.56
2.21-2.310.22521420.19273060X-RAY DIFFRACTION99.16
2.31-2.430.26261390.20933026X-RAY DIFFRACTION98.66
2.43-2.580.27541410.20673050X-RAY DIFFRACTION99.13
2.58-2.780.27041420.21763066X-RAY DIFFRACTION99.6
2.78-3.060.24141410.20523071X-RAY DIFFRACTION99.29
3.06-3.50.22931420.18433075X-RAY DIFFRACTION98.71
3.5-4.410.21841420.15363072X-RAY DIFFRACTION99.2
4.41-48.960.18331460.15613139X-RAY DIFFRACTION98.74
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)
12.18177671881-0.607783385985-1.222129898622.03377640626-0.3604770949963.38579444121-0.05988916507020.181321659975-0.18900075057-0.0508843730203-0.06543035328550.291267100949-0.15686519234-0.40512479746-0.02346581438910.1906503705920.0353390272591-0.04270746229270.23752692042-0.03065314372650.223566683286-33.9084168597-0.76010484254210.936760304
22.93210486027-0.603011392782-1.158894609052.04317648346-0.2145623192423.139664629810.00790986162199-0.0893601509209-0.140131138827-0.05055111611-0.166479855566-0.29591526398-0.04189886207040.295615393154-0.04124570672130.172278431436-0.0126651533682-0.02498633054190.217339560020.04561544052040.263117859923-15.3616188793-3.589738111976.70720348981
32.008081174650.5562546095560.5386079203742.034445363250.2015622897353.26390564388-0.0912603166314-0.03308629475040.026907293114-0.0937302059853-0.02203861450860.34490917516-0.0617808413266-0.33752136584-0.0001791886373380.2955069933540.01314694184480.03510326912890.223879279254-0.0211401273880.25675744725-37.9055928923-28.854925442124.4102257087
42.88359682861.109338833620.3079104293881.82564917190.06900115697854.561290707810.0621220921832-0.2681224507730.1104909709240.142785400784-0.231358430622-0.165217980591-0.002538601856480.601931585817-0.01865476147740.2433586084020.01875007972380.02119583785280.2951726007370.04885195823150.257500604547-22.282012254-26.542996134435.8774582733
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 127)AA1 - 1271 - 127
22(chain 'C' and resid 1 through 128)CB1 - 1281 - 128
33(chain 'B' and resid 1 through 127)BC1 - 1271 - 127
44(chain 'D' and resid 1 through 128)DD1 - 1281 - 128

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