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- PDB-5abp: SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUN... -

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Basic information

Entry
Database: PDB / ID: 5abp
TitleSUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES
ComponentsL-ARABINOSE-BINDING PROTEIN
KeywordsBINDING PROTEIN
Function / homology
Function and homology information


ABC-type monosaccharide transporter activity / L-arabinose transmembrane transport / 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
beta-D-galactopyranose / alpha-D-galactopyranose / L-arabinose-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsQuiocho, F.A. / Wilson, D.K. / Vyas, N.K.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Comparison of the Periplasmic Receptors for L-Arabinose-, D-Glucose/D-Galactose-, and D-Ribose. Structural and Functional Similarity
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
#2: Journal: Nature / Year: 1984
Title: Novel Stereospecificity of the L-Arabinose-Binding Protein
Authors: Quiocho, F.A. / Vyas, N.K.
History
DepositionDec 26, 1990Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 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)33,6113
Polymers33,2511
Non-polymers3602
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.920, 72.020, 78.020
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: 33250.996 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-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSINCE IT HAS BEEN SHOWN THAT ABP CAN BIND EITHER ALPHA OR BETA ANOMERS OF D-GALACTOSE WITH ALMOST ...SINCE IT HAS BEEN SHOWN THAT ABP CAN BIND EITHER ALPHA OR BETA ANOMERS OF D-GALACTOSE WITH ALMOST EQUAL AFFINITY, BOTH ARE PROVIDED IN THE SAME SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal grow
*PLUS
pH: 6.5 / Method: microdialysis / Details: took 10 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
255 %MPD1reservior
32 mMpotassium phosphate1reservoir
1protein1buttom

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å /
RfactorNum. reflection
obs0.132 18860
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 24 236 2576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.05
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr25

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