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- PDB-7abp: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDIN... -

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Basic information

Entry
Database: PDB / ID: 7abp
TitleSUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY
ComponentsL-ARABINOSE-BINDING PROTEIN
KeywordsBINDING PROTEINS
Function / homology
Function and homology information


L-arabinose transmembrane transport / ABC-type monosaccharide transporter activity / monosaccharide binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / carbohydrate binding / membrane
Similarity search - Function
L-arabinose-binding periplasmic protein / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-fucopyranose / beta-D-fucopyranose / L-arabinose-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsVermersch, P.S. / Tesmer, J.J.G. / Quiocho, F.A.
Citation
Journal: Biochemistry / Year: 1991
Title: Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity.
Authors: Vermersch, P.S. / Lemon, D.D. / Tesmer, J.J. / Quiocho, F.A.
#1: Journal: Nature / Year: 1989
Title: Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules
Authors: Quiocho, F.A. / Wilson, D.K. / Vyas, N.K.
#2: Journal: Nature / Year: 1984
Title: Novel Stereospecificity of the L-Arabinose-Binding Protein
Authors: Quiocho, F.A. / Vyas, N.K.
#3: Journal: J.Biol.Chem. / Year: 1982
Title: Hinge-Bending in L-Arabinose-Binding Protein. The "Venus'S-Flytrap" Model
Authors: Mao, B. / Pear, M.R. / Mccammon, J.A. / Quiocho, F.A.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of the L-Arabinose-Binding Protein from Escherichia Coli at 2.4 Angstroms Resolution
Authors: Gilliland, G.L. / Quiocho, F.A.
#5: Journal: J.Biol.Chem. / Year: 1981
Title: L-Arabinose-Binding Protein-Sugar Complex at 2.4 Angstroms Resolution. Stereochemistry and Evidence for a Structural Change
Authors: Newcomer, M.E. / Gilliand, G.L. / Quiocho, F.A.
#6: Journal: J.Biol.Chem. / Year: 1981
Title: The Radius of Gyration of L-Arabinose-Binding Protein Decreases Upon Binding of Ligand
Authors: Newcomer, M.E. / Lewis, B.A. / Quiocho, F.A.
#7: Journal: J.Biol.Chem. / Year: 1979
Title: The Thiol Group of the L-Arabinose-Binding Protein. Chromophoric Labeling and Chemical Identification of the Sugar-Binding Site
Authors: Miller /III, D.M. / Newcomer, M.E. / Quiocho, F.A.
#8: Journal: J.Biol.Chem. / Year: 1979
Title: Location of the Sugar-Binding Site of L-Arabinose-Binding Protein. Sugar Derivative Syntheses, Sugar Binding Specificity, and Difference Fourier Analyses
Authors: Newcomer, M.E. / Miller /III, D.M. / Quiocho, F.A.
#9: Journal: J.Biol.Chem. / Year: 1977
Title: The 2.8-Angstroms Resolution Structure of the L-Arabinose-Binding Protein from Escherichia Coli
Authors: Quiocho, F.A. / Gilliland, G.L. / Phillips Jr., G.N.
#10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1976
Title: Structure of L-Arabinose-Binding Protein from Escherichia Coli at 5 Angstroms Resolution and Preliminary Results at 3.5 Angstroms
Authors: Phillips Jr., G.N. / Mahajan, V.K. / Siu, A.K.Q. / Quiocho, F.A.
History
DepositionApr 25, 1991Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _chem_comp.name ..._atom_site.label_alt_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 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: L-ARABINOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5613
Polymers33,2331
Non-polymers3282
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.750, 71.830, 78.140
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 L-ARABINOSE-BINDING PROTEIN


Mass: 33232.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02924
#2: Sugar ChemComp-FCA / alpha-D-fucopyranose / alpha-D-fucose / 6-deoxy-alpha-D-galactopyranose / D-fucose / fucose / Fucose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
DFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-fucopyranoseCOMMON NAMEGMML 1.0
a-D-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FCB / beta-D-fucopyranose / beta-D-fucose / 6-deoxy-beta-D-galactopyranose / D-fucose / fucose / Fucose


Type: D-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
DFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fucopyranoseCOMMON NAMEGMML 1.0
b-D-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193
Source method: isolated from a genetically manipulated 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: 47.72 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 265.16592-16603
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
210 %PEG1drop
310 mMcitrate1drop
41 mM1dropNaBH4
50.02 %sodium azide1drop
610 mMsugar1dropD-galactose, D-fucose, L-arabinose
720 %PEG1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.67 Å / Lowest resolution: 8 Å / Num. obs: 33726 / % possible obs: 91 % / Num. measured all: 120410 / Rmerge(I) obs: 0.0595

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.67→8 Å /
RfactorNum. reflection
obs0.162 29509
Refinement stepCycle: LAST / Resolution: 1.67→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 22 193 2531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.044
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.67 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.162 / Num. reflection obs: 29509
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_planar_d0.050.067
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.050.053
X-RAY DIFFRACTIONp_mcbond_it1.51.692
X-RAY DIFFRACTIONp_scbond_it2.53.991
X-RAY DIFFRACTIONp_mcangle_it22.347
X-RAY DIFFRACTIONp_scangle_it35.88

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