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- PDB-1oge: The Structure of Bacillus subtilis RbsD complexed with Ribose 5-p... -

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Basic information

Entry
Database: PDB / ID: 1oge
TitleThe Structure of Bacillus subtilis RbsD complexed with Ribose 5-phosphate
ComponentsHIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
KeywordsTRANSPORT / RIBOSE 5-PHOSPHATE / SUGAR TRANSPORT
Function / homology
Function and homology information


D-ribose pyranase / intramolecular transferase activity / D-ribose pyranase activity / intramolecular lyase activity / D-ribose catabolic process / monosaccharide binding / cytosol
Similarity search - Function
D-ribose pyranase / RbsD-like fold / RbsD-like domain / D-ribose pyranase RbsD/L-fucose mutarotase FucU / RbsD-like superfamily / RbsD / FucU transport protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-O-phosphono-beta-D-ribofuranose / D-ribose pyranase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 2.05 Å
AuthorsKim, M.-S. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture
Authors: Kim, M.-S. / Shin, J. / Lee, W. / Lee, H.-S. / Oh, B.-H.
History
DepositionApr 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
B: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
C: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
D: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
E: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,44412
Polymers71,2225
Non-polymers1,2217
Water3,459192
1
A: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
B: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
C: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
D: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
E: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
hetero molecules

A: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
B: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
C: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
D: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
E: HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,88724
Polymers142,44410
Non-polymers2,44314
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)123.807, 108.556, 83.532
Angle α, β, γ (deg.)90.00, 128.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD / CYTOPLASMIC RIBOSE-BINDING PROTEIN RBSD


Mass: 14244.438 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria) / References: UniProt: P36946
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar
ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRBSD IS INVOLVED IN THE HIGH-AFFINITY RIBOSE MEMBRANE TRANSPORT SYSTEM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.4
30.2 M1dropNaCl
42 mMdithiothreitol1drop
520 %PEG40001reservoir
619 %isopropyl1reservoir
7100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 48339 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 2.5 %
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 30 Å / Num. measured all: 236173 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 80.7 % / Rmerge(I) obs: 0.225

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 2.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.227 --
Rwork0.194 --
obs0.194 48339 90.3 %
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 72 192 5274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.268
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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