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- PDB-5lrb: Plastidial phosphorylase from Barley in complex with acarbose -

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Basic information

Entry
Database: PDB / ID: 5lrb
TitlePlastidial phosphorylase from Barley in complex with acarbose
ComponentsAlpha-1,4 glucan phosphorylase
KeywordsTRANSFERASE / Starch / phophorylase / plastidial
Function / homology
Function and homology information


maltodextrin phosphorylase activity / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / 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-acarbose / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesHordeum vulgare var. distichum (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCuesta-Seijo, J.A. / Ruzanski, C. / Kruzewicz, K. / Palcic, M.M.
CitationJournal: PLoS ONE / Year: 2017
Title: Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development.
Authors: Cuesta-Seijo, J.A. / Ruzanski, C. / Krucewicz, K. / Meier, S. / Hagglund, P. / Svensson, B. / Palcic, M.M.
History
DepositionAug 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_struct_assembly_gen / pdbx_struct_mod_residue / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,4 glucan phosphorylase
B: Alpha-1,4 glucan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,1738
Polymers212,0272
Non-polymers2,1466
Water1,00956
1
A: Alpha-1,4 glucan phosphorylase
hetero molecules

A: Alpha-1,4 glucan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,1738
Polymers212,0272
Non-polymers2,1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8070 Å2
ΔGint-28 kcal/mol
Surface area60320 Å2
MethodPISA
2
B: Alpha-1,4 glucan phosphorylase
hetero molecules

B: Alpha-1,4 glucan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,1738
Polymers212,0272
Non-polymers2,1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8170 Å2
ΔGint-28 kcal/mol
Surface area60380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.330, 63.680, 149.330
Angle α, β, γ (deg.)90.00, 115.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 69 - 968 / Label seq-ID: 27 - 926

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-1,4 glucan phosphorylase


Mass: 106013.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare var. distichum (barley)
Production host: Escherichia coli (E. coli) / References: UniProt: F2E0G2, 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
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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.: 56 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 30% PEG4000, 0.1M Nacitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 43219 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.6
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 0.98

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LR8

5lr8


Resolution: 2.9→48.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 45.193 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24602 1297 3 %RANDOM
Rwork0.21257 ---
obs0.21358 41921 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.706 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0 Å20.48 Å2
2---3.19 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13420 0 142 56 13618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213134
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.96218946
X-RAY DIFFRACTIONr_angle_other_deg0.754330277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64851704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34224.433661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.817152398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3221579
X-RAY DIFFRACTIONr_chiral_restr0.0740.22081
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023217
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3294.1316762
X-RAY DIFFRACTIONr_mcbond_other1.3294.1316761
X-RAY DIFFRACTIONr_mcangle_it2.2626.1968451
X-RAY DIFFRACTIONr_mcangle_other2.2626.1968452
X-RAY DIFFRACTIONr_scbond_it1.4074.4097200
X-RAY DIFFRACTIONr_scbond_other1.4064.4097200
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3696.57610485
X-RAY DIFFRACTIONr_long_range_B_refined5.26539.66559425
X-RAY DIFFRACTIONr_long_range_B_other5.26539.65159416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5558 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 88 -
Rwork0.496 2831 -
obs--91.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4656-0.03240.51921.1827-0.43062.1137-0.250.2681-0.2309-0.06070.1590.0591-0.17820.00690.0910.2796-0.12170.00520.1216-0.09870.21775.64070.874549.144
21.6349-0.18880.33271.34630.28842.2543-0.2136-0.2988-0.33150.2830.1172-0.0660.09690.05310.09640.2150.09580.04270.10450.13940.27137.88655.980918.4759
31.85920.28440.05581.61990.22621.3467-0.2401-0.0192-0.21640.17170.22450.3109-0.1756-0.52580.01550.3194-0.0020.01140.35950.01840.316846.70441.826252.7053
42.2402-0.44860.01831.3045-0.32311.3061-0.2308-0.0458-0.28460.09040.1495-0.19690.01930.52140.08130.27660.1062-0.0190.33750.05610.282636.87446.817414.9318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 500
2X-RAY DIFFRACTION2B1 - 500
3X-RAY DIFFRACTION3A501 - 999
4X-RAY DIFFRACTION4B501 - 999

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