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- PDB-7qsp: Permutated C-terminal lobe of the ribose binding protein from The... -

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Basic information

Entry
Database: PDB / ID: 7qsp
TitlePermutated C-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 / Ribose ABC transporter, periplasmic ribose-binding protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 1.2Feb 7, 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
B: Ribose ABC transporter, periplasmic ribose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,42311
Polymers33,8642
Non-polymers5599
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint17 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.690, 41.970, 132.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 16932.090 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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 % sol: 27.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate, 20% (w/v) PEG3350, cryogenic additives: 20% PEG3000, 20% Ethylene-glycol, 0.2M KNO3

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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: Apr 25, 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: 1.36→39.76 Å / Num. obs: 50882 / % possible obs: 99 % / Redundancy: 10.5 % / Biso Wilson estimate: 18.76 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.026 / Rrim(I) all: 0.085 / Net I/σ(I): 13.93
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.907 / Mean I/σ(I) obs: 1 / Num. unique obs: 4875 / CC1/2: 0.322 / CC star: 0.698 / Rpim(I) all: 0.616 / Rrim(I) all: 2.008 / % possible all: 96.7

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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: 1.36→39.76 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / Phase error: 19.3755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 2100 4.13 %
Rwork0.1731 48783 -
obs0.1746 50881 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.58 Å2
Refinement stepCycle: LAST / Resolution: 1.36→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 36 196 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772171
X-RAY DIFFRACTIONf_angle_d1.04022937
X-RAY DIFFRACTIONf_chiral_restr0.0679294
X-RAY DIFFRACTIONf_plane_restr0.0098384
X-RAY DIFFRACTIONf_dihedral_angle_d13.8493790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.40.42091320.37163077X-RAY DIFFRACTION95.45
1.4-1.420.35071380.31683210X-RAY DIFFRACTION99.44
1.42-1.460.31991360.27433164X-RAY DIFFRACTION97.86
1.46-1.50.28571380.23733187X-RAY DIFFRACTION98.52
1.5-1.550.22881390.20583227X-RAY DIFFRACTION99.15
1.55-1.610.231390.18753245X-RAY DIFFRACTION99.38
1.61-1.670.22391400.18923238X-RAY DIFFRACTION99.5
1.67-1.750.20781390.17683239X-RAY DIFFRACTION99.65
1.75-1.840.2161400.16873247X-RAY DIFFRACTION99.76
1.84-1.950.21451400.16593264X-RAY DIFFRACTION99.79
1.95-2.10.18751400.15323250X-RAY DIFFRACTION98.63
2.1-2.320.17361420.15283294X-RAY DIFFRACTION99.94
2.32-2.650.19321430.15773313X-RAY DIFFRACTION99.97
2.65-3.340.19691440.16613356X-RAY DIFFRACTION99.77
3.34-39.760.21361500.16593472X-RAY DIFFRACTION98.37
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)
11.828965640260.07394572347250.2283262526971.407950070110.4206629534692.70482172230.09546092339220.0970970000457-0.215521025172-0.0220973900246-0.00280764964213-0.1128033097690.4525636126740.1293349742710.02801413258670.2014559347640.0234521627605-0.01574044862580.132163147998-0.007381758772430.14072619549315.35707395082.124220794844.83884519183
21.53548183967-0.6397182204790.02163529690161.9570580022-0.4023219634042.43787863234-0.00253353970176-0.04268196961450.063851487202-0.0502289505240.0470916072102-0.1064380179860.07367098652890.09976316450260.009112385993170.0630380915406-0.005904561913860.01027267041910.0861520193638-0.001674698687480.1119347414048.2620454571-7.6062336383628.6620095515
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 142

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain 'A' and resid 1 through 142)AA1 - 123
22(chain 'B' and resid 1 through 142)BC1 - 125

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