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- PDB-4bqf: Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PH... -

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Basic information

Entry
Database: PDB / ID: 4bqf
TitleArabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with acarbose
ComponentsALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC
KeywordsTRANSFERASE / CARBOHYDRATE METABOLISM / SELF-ASSEMBLY ON SURFACES
Function / homology
Function and homology information


1,4-alpha-oligoglucan phosphorylase activity / response to water deprivation / glycogen phosphorylase / glycogen phosphorylase activity / : / : / chloroplast / pyridoxal phosphate binding / carbohydrate metabolic process / 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
beta-acarbose / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Alpha-glucan phosphorylase 2, cytosolic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsO'Neill, E.C. / Rashid, A.M. / Stevenson, C.E.M. / Hetru, A.C. / Gunning, A.P. / Rejzek, M. / Nepogodiev, S.A. / Bornemann, S. / Lawson, D.M. / Field, R.A.
CitationJournal: Chem.Sci. / Year: 2014
Title: Sugar-Coated Sensor Chip and Nanoparticle Surfaces for the in Vitro Enzymatic Synthesis of Starch-Like Materials
Authors: O'Neill, E.C. / Rashid, A.M. / Stevenson, C.E.M. / Hetru, A.C. / Gunning, A.P. / Rejzek, M. / Nepogodiev, S.A. / Bornemann, S. / Lawson, D.M. / Field, R.A.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_unobs_or_zero_occ_atoms / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC
B: ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,54710
Polymers198,1292
Non-polymers2,4188
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-8.2 kcal/mol
Surface area58770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.249, 117.075, 94.967
Angle α, β, γ (deg.)90.00, 106.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC / ATPHS2 / ALPHA-GLUCAN PHOSPHORYLASE / H ISOZYME / STARCH PHOSPHORYLASE H / PHS2


Mass: 99064.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET151-PHS2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 LYSS / References: UniProt: Q9SD76, glycogen phosphorylase

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Sugars , 2 types, 5 molecules

#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)-beta-D-glucopyranose / beta-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: beta-acarbose
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 3 types, 347 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsALPHA-ACARBOSE (ACR): CRYSTAL WAS SOAKED FOR 1 WEEK IN A 1 MILLIMOLAR SOLUTION OF ACARBOSE MADE UP ...ALPHA-ACARBOSE (ACR): CRYSTAL WAS SOAKED FOR 1 WEEK IN A 1 MILLIMOLAR SOLUTION OF ACARBOSE MADE UP IN CRYSTALLIZATION WELL SOLUTION PYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLY LINKED TO LYS 687 OF CORRESPONDING PROTEIN CHAIN ALPHA-D-GLUCOSE (GLC): DENSITY PRESENT FOR ISOLATED MONOSACCHARIDES. THESE WERE MODELLED AS GLUCOSE MOLECULES, BUT WERE MOST LIKELY PART OF DISORDERED ACARBOSE MOLECULES.
Sequence detailsA 33-RESIDUE HEXAHISTIDINE AFFINITY TAG IS APPENDED TO THE N-TERMINUS OF THE WILD-TYPE SEQUENCE AND ...A 33-RESIDUE HEXAHISTIDINE AFFINITY TAG IS APPENDED TO THE N-TERMINUS OF THE WILD-TYPE SEQUENCE AND IS DERIVED FROM THE PET151 EXPRESSION VECTOR

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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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML ...Details: CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML IN 12.5 MM HEPES PH 7.5, 25 MM NACL WAS MIXED WITH 1 MICROLITRE OF THE WELL SOLUTION TO GIVE THE FINAL DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→66.42 Å / Num. obs: 69673 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPB

1gpb


Resolution: 2.35→60.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 18.638 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24024 3670 5 %RANDOM
Rwork0.1838 ---
obs0.1866 69673 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å2-2.09 Å2
2---2.55 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.35→60.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13030 0 138 344 13512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213547
X-RAY DIFFRACTIONr_bond_other_d0.0040.029159
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.96218420
X-RAY DIFFRACTIONr_angle_other_deg1.118322273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17651668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76224.06633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.315152244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.491589
X-RAY DIFFRACTIONr_chiral_restr0.090.22043
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115071
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022819
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 259 -
Rwork0.281 5035 -
obs--99.68 %
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)
10.6557-0.03260.27680.739-0.30681.23830.0375-0.0064-0.16560.09910.01180.03910.0678-0.0131-0.04930.0747-0.0054-0.00110.0486-0.0180.09338.3495-33.051336.5525
20.53240.34630.42871.190.08791.1789-0.04340.1466-0.0134-0.00890.0143-0.1165-0.12410.20390.02910.0786-0.02140.01420.12720.00030.074452.743-15.750227.6985
30.6691-0.3680.26922.2530.69714.4321-0.04430.22270.0567-0.22050.06770.1257-0.2502-0.228-0.02330.2663-0.0573-0.01270.22130.04250.111348.1194-1.44119.8707
41.73781.69180.15261.95180.20410.5141-0.15460.16560.1044-0.2360.12460.1334-0.10730.07820.030.11050.02310.00230.0868-0.0170.068731.6638-23.905213.4518
52.07241.83060.35035.66493.09012.62970.2159-0.23970.05490.6617-0.18430.22150.3403-0.1077-0.03160.12190.01120.03120.08040.00410.097211.7602-32.127330.4187
60.8881-0.69770.59262.21590.30311.90480.0074-0.06340.16480.1298-0.10080.32720.0276-0.26320.09340.0683-0.01550.05250.0828-0.02910.200411.4448-16.465630.0815
70.9632-0.12660.50733.77630.55811.32950.0083-0.02050.3371-0.1598-0.17460.343-0.2872-0.11470.16630.08250.03480.01360.1078-0.01340.18189.1423-10.057619.004
84.73282.1725-0.0351.2399-0.11280.0695-0.09830.45840.0343-0.11360.1101-0.02190.03360.0862-0.01180.12240.0146-0.00060.1672-0.02440.031131.3172-33.037213.2876
90.3773-0.02970.16041.01350.26780.94470.03280.0863-0.13120.0077-0.0326-0.11290.05270.1438-0.00020.0679-0.0247-0.03580.07250.02640.124955.5899-29.178457.8084
105.07850.3885.45690.7098-0.60937.4202-0.154-0.29440.27560.0415-0.06060.0776-0.2363-0.28260.21460.13080.00770.06410.0592-0.02770.059744.9334-6.552450.9964
110.6253-1.40330.04653.5328-0.07841.8237-0.0199-0.0797-0.04050.21040.00470.12430.07370.08080.01520.1348-0.04710.02850.1037-0.00140.013344.7361-15.048275.2647
122.1021-1.1620.49021.6911-0.5250.271-0.286-0.25030.05370.41440.2166-0.1411-0.13880.02870.06930.2519-0.0211-0.11570.17750.0510.10865.9991-22.064179.8574
132.7377-0.61021.16843.6078-0.13812.3642-0.05440.0502-0.0614-0.23110.1101-0.3233-0.07580.1605-0.05560.1921-0.1469-0.01040.22890.0580.165187.3377-13.566560.4652
141.1380.1330.88962.0439-0.95861.2532-0.22190.0766-0.0232-0.07030.1628-0.171-0.1532-0.01950.05910.1326-0.0887-0.02050.20090.04310.139381.7127-20.853267.0234
150.88130.20540.54543.1939-0.65432.4237-0.2478-0.030.23860.32570.1502-0.2565-0.6376-0.01410.09750.2726-0.0507-0.16510.2920.02920.313888.5864-7.057873.8952
163.7926-0.8509-0.0790.78240.18720.0804-0.1931-0.23530.09230.17260.1254-0.0364-0.01080.05750.06770.1813-0.0163-0.08360.09280.07930.158768.7935-32.991178.7122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 182
2X-RAY DIFFRACTION2A183 - 379
3X-RAY DIFFRACTION3A380 - 433
4X-RAY DIFFRACTION4A434 - 526
5X-RAY DIFFRACTION5A527 - 573
6X-RAY DIFFRACTION6A574 - 694
7X-RAY DIFFRACTION7A695 - 805
8X-RAY DIFFRACTION8A806 - 841
9X-RAY DIFFRACTION9B15 - 248
10X-RAY DIFFRACTION10B249 - 292
11X-RAY DIFFRACTION11B293 - 404
12X-RAY DIFFRACTION12B405 - 548
13X-RAY DIFFRACTION13B549 - 640
14X-RAY DIFFRACTION14B641 - 706
15X-RAY DIFFRACTION15B707 - 803
16X-RAY DIFFRACTION16B804 - 841

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