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- PDB-2ecp: THE CRYSTAL STRUCTURE OF THE E. COLI MALTODEXTRIN PHOSPHORYLASE C... -

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Basic information

Entry
Database: PDB / ID: 2ecp
TitleTHE CRYSTAL STRUCTURE OF THE E. COLI MALTODEXTRIN PHOSPHORYLASE COMPLEX
ComponentsMALTODEXTRIN PHOSPHORYLASE
KeywordsACARBOSE / DIABETES / PHOSPHORYLASE / MALP / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / PYRIDOXAL-5'-PHOSPHATE / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsO'Reilly, M. / Watson, K.A. / Johnson, L.N.
Citation
Journal: Biochemistry / Year: 1999
Title: The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex.
Authors: O'Reilly, M. / Watson, K.A. / Johnson, L.N.
History
DepositionOct 27, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
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: MALTODEXTRIN PHOSPHORYLASE
B: MALTODEXTRIN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,5238
Polymers180,5542
Non-polymers1,9706
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-32 kcal/mol
Surface area57400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.490, 105.840, 217.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.666, 0.745, 0.038), (0.74, 0.654, 0.155), (0.091, 0.131, -0.987)
Vector: 13.423, -16.991, 121.186)

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Components

#1: Protein MALTODEXTRIN PHOSPHORYLASE / ECP / MALP


Mass: 90276.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Tissue: MUSCLE / Cell line: DELTA MALA518 / Cellular location: CYTOPLASM / Plasmid: PMAP101 / Cell line (production host): DELTA MALA518 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P00490, glycogen phosphorylase
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 55 %
Description: MALP NATIVE STRUCTURE USED AS STARTING MODEL FOR MOLECULAR REPLACEMENT.
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
230 mMacarbose1reservoir
325-28 %(w/v)PEG33501reservoir
40.1-0.6 M1reservoirLiCl
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: DIAMOND C(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.95→33.6 Å / Num. obs: 33657 / % possible obs: 88.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.3 / % possible all: 78.2
Reflection shell
*PLUS
% possible obs: 78.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.57 / Details: TIGHT NCS RESTRAINTS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 852 2.5 %RANDOM
Rwork0.241 ---
obs-32524 88.9 %-
Displacement parametersBiso mean: 53.6 Å2
Refinement stepCycle: LAST / Resolution: 2.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12738 0 130 93 12961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it1.82
X-RAY DIFFRACTIONp_mcangle_it3.023
X-RAY DIFFRACTIONp_scbond_it2.92
X-RAY DIFFRACTIONp_scangle_it4.713
X-RAY DIFFRACTIONp_plane_restr0.02230.03
X-RAY DIFFRACTIONp_chiral_restr0.1230.15
X-RAY DIFFRACTIONp_singtor_nbd0.2020.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.2010.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor21.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.120
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.6

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