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- PDB-1ba2: D67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1ba2
TitleD67R MUTANT OF D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI
ComponentsD-RIBOSE-BINDING PROTEIN
KeywordsTRANSPORT / CHEMOTAXIS / PERIPLASM
Function / homology
Function and homology information


D-ribose transmembrane transport / monosaccharide binding / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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
Ribose import binding protein RbsB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBjorkman, A.J. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Multiple open forms of ribose-binding protein trace the path of its conformational change.
Authors: Bjorkman, A.J. / Mowbray, S.L.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Identical Mutations at Corresponding Positions in Two Homologous Proteins with Nonidentical Effects
Authors: Bjorkman, A.J. / Binnie, R.A. / Cole, L.B. / Zhang, H. / Hermodson, M.A. / Mowbray, S.L.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: 1.7 A X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli
Authors: Mowbray, S.L. / Cole, L.B.
#4: Journal: Protein Sci. / Year: 1992
Title: Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations that Affect Chemotaxis and Transport
Authors: Binnie, R.A. / Zhang, H. / Mowbray, S. / Hermodson, M.A.
History
DepositionApr 19, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-RIBOSE-BINDING PROTEIN
B: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,0992
Polymers57,0992
Non-polymers00
Water6,071337
1
A: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5501
Polymers28,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-RIBOSE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5501
Polymers28,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.801, 89.944, 112.276
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: 28549.529 Da / Num. of mol.: 2 / Mutation: D67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Cellular location: PERIPLASMIC / Plasmid: PB35X / Cellular location (production host): PERIPLASMIC / Gene (production host): RBSB / Production host: Escherichia coli (E. coli) / Strain (production host): MK-6- / References: UniProt: P02925
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Description: RESOLUTION LIMITS 8-4 ANGSTROMS IN THE SEARCHES.
Crystal growMethod: vapor diffusion / pH: 7
Details: VAPOR DIFFUSION OF DROPS CONTAINING 7.5 MG/ML PROTEIN AGAINST A RESERVOIR OF 24% PEG4000, 100 MM TRIS-HCL, PH 7., pH 7.0, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
224 %PEG40001reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→19 Å / Num. obs: 27352 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.36 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 21.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 7.6 / % possible all: 70
Reflection shell
*PLUS
% possible obs: 70 %

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEARCH MODELS REPRESENTING ALL NON-HYDROGEN ATOMS FROM DOMAIN 1 (RESIDUES 1-103 AND 236-264) AND DOMAIN 2 (RESIDUES 104-235 AND 265-271) OF PDB ENTRY 2DRI WERE USED SEPARATELY.

2dri


Resolution: 2.1→19 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -10 %RANDOM
Rwork0.199 ---
obs-27352 94.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 0 337 4684
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 27352 / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_deg1.85
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.6
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.73

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