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- PDB-1ahp: OLIGOSACCHARIDE SUBSTRATE BINDING IN ESCHERICHIA COLI MALTODEXTRI... -

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Basic information

Entry
Database: PDB / ID: 1ahp
TitleOLIGOSACCHARIDE SUBSTRATE BINDING IN ESCHERICHIA COLI MALTODEXTRIN PHSPHORYLASE
ComponentsE.COLI MALTODEXTRIN PHOSPHORYLASE
KeywordsECOLI / PHOSPHORYLASE / OLIGOSACCHARIDE / INDUCED-FIT / SUBSTRATE / MALTODEXTRIN / STACKING
Function / homology
Function and homology information


maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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-maltose / PYRIDOXAL-5'-PHOSPHATE / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsO'Reilly, M. / Watson, K.A. / Schinzel, R. / Palm, D. / Johnson, L.N.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase.
Authors: O'Reilly, M. / Watson, K.A. / Schinzel, R. / Palm, D. / Johnson, L.N.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 5, 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 / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / 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_database_status.process_site / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E.COLI MALTODEXTRIN PHOSPHORYLASE
B: E.COLI MALTODEXTRIN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,28510
Polymers180,7302
Non-polymers1,5558
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-60 kcal/mol
Surface area54500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.200, 112.400, 121.700
Angle α, β, γ (deg.)90.00, 119.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.726932, -0.000378, -0.686708), (-0.031532, -0.998926, 0.033929), (-0.685985, 0.046317, 0.72614)
Vector: 69.40787, -0.83145, 27.7496)

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Components

#1: Protein E.COLI MALTODEXTRIN PHOSPHORYLASE / MALP


Mass: 90365.008 Da / Num. of mol.: 2 / Mutation: N112A
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL PHOSPHATE COFACTOR ATTACHED TO LYS 645 / Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P00490, glycogen phosphorylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M NATARTRATE, PH 6.4, 24% PEG 3350, 1MM SODIUM AZIDE, 16 DEG CELCIUS, 50MM MALTOHEXAOSE STOCK, 16.5MG/ML PROTEIN STOCK, HANGING DROPS 1MICRO LITRE WELL & 0.5 MICRO LITRE MALTOHEXAOSE 0.5 ...Details: 0.1M NATARTRATE, PH 6.4, 24% PEG 3350, 1MM SODIUM AZIDE, 16 DEG CELCIUS, 50MM MALTOHEXAOSE STOCK, 16.5MG/ML PROTEIN STOCK, HANGING DROPS 1MICRO LITRE WELL & 0.5 MICRO LITRE MALTOHEXAOSE 0.5 MICRO LITRE PROTEIN, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-24 %PEG33501reservoir
21 mMsodium azide1reservoir
30.5-0.8 Msodium chloride1reservoir
40.1 Msodium tartrate1reservoir
610-12.5 mMmaltohexaose1protein
710-12 %PEG33501protein
80.5 mMsodium azide1protein
90.25-0.4 Msodium chloride1protein
5MalP N133A1protein0.005ml
100.05 Msodium tartrate1protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 33108 / % possible obs: 81.7 % / Observed criterion σ(I): 1 / Redundancy: 1.6 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.08 Å / Redundancy: 1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 1.9 / % possible all: 80.3
Reflection
*PLUS
Num. measured all: 52324

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MALP NATIVE STRUCTURE

Resolution: 3→10 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED B / Cross valid method: THROUGHOUT / σ(F): 1
Details: COORDINATES FOR MOLECULE A WERE PROVIDED BY THE DEPOSITOR. MOLECULE B WAS GENERATED BY THE PDB USING NCS SYMMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 608 2 %RANDOM
Rwork0.232 ---
obs0.232 29121 73 %-
Displacement parametersBiso mean: 25.4 Å2
Refine analyze
ObsFree
Luzzati coordinate error0.25 Å-
Luzzati d res low10 Å-
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12732 0 98 0 12830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.357 59 1.2 %
Rwork0.318 2844 -
obs--57 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2SO4.PARAMSO4.TOP
X-RAY DIFFRACTION3PLP.PARAMPLP.TOP
X-RAY DIFFRACTION4OLI.PARAMOLI.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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