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- PDB-1l6i: Crystal Structure of the Maltodextrin Phosphorylase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1l6i
TitleCrystal Structure of the Maltodextrin Phosphorylase complexed with the products of the enzymatic reaction between glucose-1-phosphate and maltopentaose
ComponentsMALTODEXTRIN PHOSPHORYLASE
KeywordsTRANSFERASE / phosphorylase / enzymatic catalysis / substrate complex
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 / cytosol / cytoplasm
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-maltopentaose / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / : / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsGeremia, S. / Campagnolo, M. / Schinzel, R. / Johnson, L.N.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase
Authors: Geremia, S. / Campagnolo, M. / Schinzel, R. / Johnson, L.N.
History
DepositionMar 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / 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 / struct_asym / struct_conn / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: MALTODEXTRIN PHOSPHORYLASE
B: MALTODEXTRIN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,4368
Polymers181,0942
Non-polymers2,3426
Water21,6721203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-1 kcal/mol
Surface area56050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.331, 105.937, 218.895
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 PHOSPHORYLASE


Mass: 90547.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PMAP101 / Production host: Escherichia coli (E. coli) / Strain (production host): DELTA MALA518
References: GenBank: 606352, UniProt: P00490*PLUS, glycogen phosphorylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#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.: 1203 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: peg 4000, t / pH: 8.5
Details: PEG 4000, TRIS, Lithium Chloride, Glucose-1-phosphate, pH 8.5, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16.0 mg/mlprotein1drop
2100 mMGlc1P1drop
327 %(w/v)PEG40001reservoir
40.1 M1reservoirLiCl
50.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.2→19 Å / Num. all: 81626 / Num. obs: 81626 / % possible obs: 91.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 34.034 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11231 / % possible all: 87.4
Reflection
*PLUS
Lowest resolution: 19 Å / Num. measured all: 413101
Reflection shell
*PLUS
% possible obs: 87.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
DMmodel building
REFMACrefinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1L5V

1l5v


Resolution: 2.2→20 Å / SU B: 7.6643 / SU ML: 0.19493 / Cross valid method: THROUGHOUT / ESU R: 0.36121 / ESU R Free: 0.23644 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24312 4167 5 %RANDOM
Rwork0.19736 ---
all0.19971 81515 --
obs0.19971 81515 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 35.156 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å20 Å20 Å2
2---1.09 Å20 Å2
3---5.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12780 0 152 1203 14135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.021
X-RAY DIFFRACTIONp_mcbond_it1.0581.5
X-RAY DIFFRACTIONp_mcangle_it1.8332
X-RAY DIFFRACTIONp_scbond_it3.1253
X-RAY DIFFRACTIONp_scangle_it4.7294.5
X-RAY DIFFRACTIONp_angle_deg2.2241.948
X-RAY DIFFRACTIONp_chiral_restr0.1560.2
X-RAY DIFFRACTIONp_plane_restr0.0110.02
Refinement
*PLUS
Num. reflection obs: 78791 / Rfactor obs: 0.2 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_deg1.9

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