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- PDB-1ogd: The Structure of Bacillus subtilis RbsD complexed with D-ribose -

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Basic information

Entry
Database: PDB / ID: 1ogd
TitleThe Structure of Bacillus subtilis RbsD complexed with D-ribose
ComponentsHIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
KeywordsTRANSPORT / RIBOSE / SUGAR TRANSPORT
Function / homology
Function and homology information


D-ribose pyranase / D-ribose pyranase activity / intramolecular transferase 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
beta-D-ribopyranose / D-ribose pyranase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 1.95 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)72,04412
Polymers71,2225
Non-polymers8227
Water3,729207
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)144,08724
Polymers142,44410
Non-polymers1,64314
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)123.515, 108.656, 83.308
Angle α, β, γ (deg.)90.00, 128.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2024-

HOH

21E-2025-

HOH

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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 / Details: D-RIBOSE / Source: (natural) BACILLUS SUBTILIS (bacteria) / References: UniProt: P36946
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar
ChemComp-RIP / beta-D-ribopyranose / Ribose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
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: 1.95→30 Å / Num. obs: 62406 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 %
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. measured all: 295120 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.362

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.211 --
Rwork0.198 --
obs0.198 62406 97.6 %
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 52 207 5269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
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_deg1.342
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
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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