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- PDB-2dri: PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 2dri
TitlePROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS
ComponentsD-RIBOSE-BINDING PROTEIN
KeywordsSUGAR TRANSPORT
Function / homology
Function and homology information


D-ribose transmembrane transport / monosaccharide binding / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transmembrane transport / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-ribopyranose / Ribose import binding protein RbsB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsMowbray, S.L. / Cole, L.B.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis.
Authors: Bjorkman, A.J. / Binnie, R.A. / Zhang, H. / Cole, L.B. / Hermodson, M.A. / Mowbray, S.L.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: 1.7 Angstroms X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli
Authors: Mowbray, S.L. / Cole, L.B.
#2: Journal: Protein Sci. / Year: 1992
Title: Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations which Affect Chemotaxis and Transport
Authors: Binnie, R.A. / Zhang, H. / Mowbray, S. / Hermodson, M.A.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Preliminary X-Ray Data for the Periplasmic Ribose Receptor from Escherichia Coli
Authors: Mahendroo, M. / Cole, L.B. / Mowbray, S.L.
History
DepositionSep 23, 1994Processing site: BNL
SupersessionJan 26, 1995ID: 1DRI
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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
Revision 1.5Feb 14, 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

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Assembly

Deposited unit
A: D-RIBOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6582
Polymers28,5071
Non-polymers1501
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.920, 88.990, 40.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-RIBOSE-BINDING PROTEIN


Mass: 28507.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02925
#2: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
132 %(w/v)PEG40001drop
290 mMsodium phosphate1drop
38 mMribose1drop
426 %PEG40001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 32471 / % possible obs: 95 % / Observed criterion σ(I): 1 / Num. measured all: 109138 / Rmerge(I) obs: 0.058 / Biso Wilson estimate: 24.9 Å2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→7.5 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 32471
Refinement stepCycle: LAST / Resolution: 1.6→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 20 648 3133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.11
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.11

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