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- PDB-7pu4: Crystal structure of the dimer RBP-N and RBP-Trunc from Thermotog... -

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Basic information

Entry
Database: PDB / ID: 7pu4
TitleCrystal structure of the dimer RBP-N and RBP-Trunc from Thermotoga maritima Ribose Binding Protein
Components(Ribose ABC transporter, periplasmic ribose-binding protein) x 2
KeywordsSUGAR BINDING PROTEIN / Periplasmic Binding Protein / Substrate Binding Protein / Ribose / ligand binding
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / monosaccharide binding / Periplasmic binding protein-like I / transmembrane transport / outer membrane-bounded periplasmic space / Ribose ABC transporter, periplasmic ribose-binding protein
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsRomero-Romero, S. / Michel, F. / Hocker, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC Consolidator grant 647548 Protein LegoEuropean Union
CitationJournal: Protein Sci. / Year: 2023
Title: Retracing the evolution of a modern periplasmic binding protein.
Authors: Michel, F. / Romero-Romero, S. / Hocker, B.
History
DepositionSep 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,7934
Polymers72,7934
Non-polymers00
Water6,882382
1
A: Ribose ABC transporter, periplasmic ribose-binding protein
B: Ribose ABC transporter, periplasmic ribose-binding protein


Theoretical massNumber of molelcules
Total (without water)36,3962
Polymers36,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribose ABC transporter, periplasmic ribose-binding protein
D: Ribose ABC transporter, periplasmic ribose-binding protein


Theoretical massNumber of molelcules
Total (without water)36,3962
Polymers36,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.210, 84.200, 103.800
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: 14873.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain A (RBP-N) & B (RBP-Trunc) form a dimer reconstructing the canonical Ribose Binding Protein
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: TM_0958 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X053
#2: Protein Ribose ABC transporter, periplasmic ribose-binding protein


Mass: 21522.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain A (RBP-N) & B (RBP-Trunc) form a dimer reconstructing the canonical Ribose Binding Protein
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: TM_0958 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X053
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH: 7.5, PEG 20000 15% w/v, RBP-N and RBP-Trunc equimolarly mixed at 0.5 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 26, 2021
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: 1.69→39.01 Å / Num. obs: 64629 / % possible obs: 99.76 % / Redundancy: 13.3 % / Biso Wilson estimate: 30.55 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1218 / Rpim(I) all: 0.03456 / Rrim(I) all: 0.1267 / Net I/σ(I): 14.25
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 6298 / CC1/2: 0.318 / CC star: 0.695 / Rpim(I) all: 1.104 / Rrim(I) all: 1.196 / % possible all: 98.39

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FN9

2fn9


Resolution: 1.69→39.01 Å / SU ML: 0.3135 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.7574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 2097 3.25 %
Rwork0.2062 62476 -
obs0.2073 64573 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.08 Å2
Refinement stepCycle: LAST / Resolution: 1.69→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 0 382 4755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084465
X-RAY DIFFRACTIONf_angle_d0.89226073
X-RAY DIFFRACTIONf_chiral_restr0.0569679
X-RAY DIFFRACTIONf_plane_restr0.0073796
X-RAY DIFFRACTIONf_dihedral_angle_d5.8701619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.55841330.49343946X-RAY DIFFRACTION95.44
1.73-1.770.44331380.40944102X-RAY DIFFRACTION99.84
1.77-1.820.40611380.36694112X-RAY DIFFRACTION99.95
1.82-1.870.37921390.33314141X-RAY DIFFRACTION99.93
1.87-1.930.26721380.30344121X-RAY DIFFRACTION99.91
1.93-20.26781390.28294137X-RAY DIFFRACTION99.98
2-2.080.28971390.24344156X-RAY DIFFRACTION99.95
2.08-2.180.31741400.23494166X-RAY DIFFRACTION99.93
2.18-2.290.26161390.22474133X-RAY DIFFRACTION99.95
2.29-2.440.25211400.21144179X-RAY DIFFRACTION99.98
2.44-2.620.30141400.21374182X-RAY DIFFRACTION100
2.62-2.890.25761410.21364194X-RAY DIFFRACTION100
2.89-3.30.25781420.19774230X-RAY DIFFRACTION100
3.3-4.160.19191430.16194252X-RAY DIFFRACTION100
4.16-39.010.16941480.16354425X-RAY DIFFRACTION99.52
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)
11.400184626640.2851164237360.2398967325481.706593400110.3161953153322.85083486433-0.0747360498730.02277106296980.1737695027940.0552824404644-0.074138859986-0.21368535219-0.6529585141860.0617726413841-0.04532702969230.516234745866-0.0207513813372-0.05124396117830.238555692681-0.02530691377630.313114676928-11.28237803068.50067884088-29.4871530141
22.870224184730.7666562729470.1009641817841.420752109680.3230606068711.494980859360.167330226721-0.00995587497811-0.5000062068590.0395904214592-0.013787379944-0.6046436508330.06718735230750.387314814053-0.1084043468780.5669831884540.0244646847405-0.0700730318640.358849052102-0.0669962802830.5140124378643.73231129611.1019887392-19.1622181801
31.125406350260.1761191740810.07858445011741.245550771120.7527109876252.685722307830.0569605058145-0.0906332459755-0.2360830484630.162834047926-0.151871926490.06121895821820.565070350331-0.4452674618360.1657443299490.474120581544-0.08499946213750.01356088765040.3566664084830.02065585859050.278700815405-25.8064323409-8.81211619338-11.5082475915
40.776631629916-0.108016402329-0.8207310762591.39081295481.192964090873.016370469150.0484561272555-0.0459251724377-0.0117200591611-0.0495046667347-0.1032058972940.132246498682-0.188211700444-0.1062644913850.02715258591960.2758692764150.024797820527-0.04411352637060.2313546618610.0008466275754910.214736525984-23.928115840710.6111864089-0.360792319804
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 2 through 126)AA2 - 1261 - 125
22(chain 'B' and resid 16 through 176)BB16 - 1761 - 161
33(chain 'C' and resid 1 through 123)CC1 - 1231 - 123
44(chain 'D' and resid 11 through 175)DD11 - 1751 - 165

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