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- PDB-1ez9: STRUCTURE OF MALTOTETRAITOL BOUND TO OPEN-FORM MALTODEXTRIN BINDI... -

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Basic information

Entry
Database: PDB / ID: 1ez9
TitleSTRUCTURE OF MALTOTETRAITOL BOUND TO OPEN-FORM MALTODEXTRIN BINDING PROTEIN IN P1 CRYSTAL FORM
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN
KeywordsSUGAR BINDING PROTEIN / protein-carbohydrate complex
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDuan, X. / Quiocho, F.A.
CitationJournal: Biochemistry / Year: 2002
Title: Structural evidence for a dominant role of nonpolar interactions in the binding of a transport/chemosensory receptor to its highly polar ligands.
Authors: Duan, X. / Quiocho, F.A.
History
DepositionMay 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: MALTOSE-BINDING PERIPLASMIC PROTEIN
B: MALTOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8394
Polymers81,5062
Non-polymers1,3332
Water13,745763
1
A: MALTOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4202
Polymers40,7531
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MALTOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4202
Polymers40,7531
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.745, 57.900, 64.594
Angle α, β, γ (deg.)89.31, 81.78, 71.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MALTOSE-BINDING PERIPLASMIC PROTEIN / MALTODEXTRIN-BINDING PROTEIN


Mass: 40753.152 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Strain: K12 / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-D-glucose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[o2122h][a2122h-1a_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 3350, MES, sodium azide, maltotetraitol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.5 mg/mlMBP1drop
21 mMmaltotetraitol1drop
320 %PEG33501droppH6.6
430 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 55586 / Num. obs: 51060 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 79.8
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 91.9 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.041

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.9→15 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.235 5107 Random
Rwork0.192 --
all-55586 -
obs-51060 -
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5756 0 90 763 6609
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / σ(F): 2 / Rfactor obs: 0.192 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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