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- PDB-5lra: Plastidial phosphorylase PhoI from barley in complex with maltote... -

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Basic information

Entry
Database: PDB / ID: 5lra
TitlePlastidial phosphorylase PhoI from barley in complex with maltotetraose
ComponentsAlpha-1,4 glucan phosphorylase
KeywordsTRANSFERASE / Starch / phosphorylase / 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-maltose / PYRIDOXAL-5'-PHOSPHATE / Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesHordeum vulgare var. distichum (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCuesta-Seijo, J.A. / Ruzanski, C. / Krucewicz, 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 1.1May 8, 2019Group: Data collection / Derived calculations / Category: pdbx_data_processing_status / struct_conn
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 / 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 / pdbx_validate_close_contact / 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 / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)214,5408
Polymers212,0272
Non-polymers2,5126
Water84747
1
A: Alpha-1,4 glucan phosphorylase
hetero molecules

A: Alpha-1,4 glucan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,5408
Polymers212,0272
Non-polymers2,5126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10750 Å2
ΔGint18 kcal/mol
Surface area57950 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)214,5408
Polymers212,0272
Non-polymers2,5126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10800 Å2
ΔGint18 kcal/mol
Surface area58240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.690, 63.150, 148.190
Angle α, β, γ (deg.)90.00, 114.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1,4 glucan phosphorylase


Mass: 106013.734 Da / Num. of mol.: 2 / Fragment: UNP residues 44-968
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 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: 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
#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.: 47 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG4000, 0.1M Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 38803 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 1.13 / Num. unique all: 6756

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Processing

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

5lrb


Resolution: 3→49.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 47.956 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24286 1165 3 %RANDOM
Rwork0.19483 ---
obs0.19626 37637 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.192 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-1.36 Å2
2--3.07 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 3→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13424 0 166 47 13637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213129
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.96518972
X-RAY DIFFRACTIONr_angle_other_deg0.791330236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86551702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50424.485660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.224152397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7531577
X-RAY DIFFRACTIONr_chiral_restr0.060.22092
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023202
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_it1.594.9136760
X-RAY DIFFRACTIONr_mcbond_other1.594.9136759
X-RAY DIFFRACTIONr_mcangle_it2.6617.3718448
X-RAY DIFFRACTIONr_mcangle_other2.6617.3718449
X-RAY DIFFRACTIONr_scbond_it1.7365.1867220
X-RAY DIFFRACTIONr_scbond_other1.7365.1867221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9357.71710515
X-RAY DIFFRACTIONr_long_range_B_refined6.20547.10160065
X-RAY DIFFRACTIONr_long_range_B_other6.20347.10160060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 85 -
Rwork0.37 2725 -
obs--99.86 %
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)
12.62030.25811.11741.1836-0.30592.1697-0.18940.5965-0.5517-0.08730.2019-0.007-0.13580.1602-0.01250.2068-0.09310.03510.1962-0.16690.201974.9760.81149.056
23.2984-0.29181.05941.18960.06022.1458-0.1182-0.7819-0.8950.24790.15440.05240.0317-0.1228-0.03620.13570.07760.0680.2180.25070.317.9255.90918.257
33.3290.77920.51071.07630.15561.974-0.2573-0.0353-0.3293-0.01160.23430.2346-0.39-0.53420.0230.31130.027-0.00610.3421-0.01790.272246.2171.90752.455
44.0909-1.03870.7340.902-0.2641.9489-0.2683-0.053-0.51560.1910.209-0.1327-0.35030.44840.05930.27970.035-0.04550.30250.04320.271536.6716.89814.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 495
2X-RAY DIFFRACTION2B69 - 495
3X-RAY DIFFRACTION3A553 - 969
4X-RAY DIFFRACTION4B501 - 969

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