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- PDB-1elj: THE CRYSTAL STRUCTURE OF LIGANDED MALTODEXTRIN-BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 1elj
TitleTHE CRYSTAL STRUCTURE OF LIGANDED MALTODEXTRIN-BINDING PROTEIN FROM PYROCOCCUS FURIOSUS
ComponentsMALTODEXTRIN-BINDING PROTEIN
KeywordsSUGAR BINDING PROTEIN / protein-carbohydrate complex / maltose binding protein / MBP fold / ABC transporter fold / thermophilic protein
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
Similarity search - Function
Bacterial extracellular solute-binding protein / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / Maltotriose-binding protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsEvdokimov, A.G. / Anderson, E.D. / Routzahn, K.M. / Waugh, D.S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural basis for oligosaccharide recognition by Pyrococcus furiosus maltodextrin-binding protein.
Authors: Evdokimov, A.G. / Anderson, D.E. / Routzahn, K.M. / Waugh, D.S.
History
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn / Item: _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTODEXTRIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9405
Polymers43,1471
Non-polymers7934
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.118, 68.832, 127.726
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 MALTODEXTRIN-BINDING PROTEIN


Mass: 43147.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PKM800 / Production host: Escherichia coli (E. coli) / References: UniProt: P58300
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMALTOTRIOSE IS A TRISACCHARIDE, COMPOSED OF THREE GLUCOPYRANOSIDE UNITS LINKED BY ALPHA 1->4 BONDS. ...MALTOTRIOSE IS A TRISACCHARIDE, COMPOSED OF THREE GLUCOPYRANOSIDE UNITS LINKED BY ALPHA 1->4 BONDS. IN OUR STRUCTURE WE OBSERVE THAT THE REDUCING END OF THE MOLECULE IS DISORDERED BETWEEN TWO ANOMERIC FORMS - ALPHA AND BETA. THIS IS WHY GLC 1001 HAS TWO ANOMERIC OXYGENS, EACH HAVING PARTIAL OCCUPANCY.

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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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: reservoir: 2.4 M ammonium sulfate, 0.1 M bicine-hcl. drop: 6 mg/ml protein 1:1 with reservoir, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
22.4 Mammonium sulfate1reservoir
30.1 Mbicine1reservoir
40.1 %(v/v)beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 42983 / Num. obs: 35220 / % possible obs: 80 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.08
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.23 / Num. unique all: 2996 / % possible all: 84.9
Reflection
*PLUS
Num. obs: 42983 / % possible obs: 91.88 % / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.85→100 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used conjugated gradient least squares proce
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 2253 -RANDOM
Rwork0.1957 ---
all0.1957 42982 --
obs0.1842 38331 89 %-
Refinement stepCycle: LAST / Resolution: 1.85→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 50 387 3477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d1.2
X-RAY DIFFRACTIONs_bond_d0.07
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 4 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.07
X-RAY DIFFRACTIONs_angle_d1.2

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