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- PDB-2av6: X-Ray studies on maltodextrin phosphorylase complexes: recognitio... -

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Basic information

Entry
Database: PDB / ID: 2av6
TitleX-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family
ComponentsMaltodextrin phosphorylase
KeywordsTRANSFERASE / maltopentaose / carbohydrate recognition / phosphorylase mechanism / ternary complexes with natural and inhibitory substrates
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 / cytoplasm / 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
NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGeremia, S. / Campagnolo, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: X-ray studies on ternary complexes of maltodextrin phosphorylase.
Authors: Campagnolo, M. / Campa, C. / Zorzi, R.D. / Wuerges, J. / Geremia, S.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 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 2.2Oct 25, 2023Group: 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

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Assembly

Deposited unit
A: Maltodextrin phosphorylase
B: Maltodextrin phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3708
Polymers181,0942
Non-polymers2,2766
Water20,6271145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint17 kcal/mol
Surface area56500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.957, 105.614, 218.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B
391A
401B
411A
421B
431A
441B
451A
461B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERPRO1AA1 - 31 - 3
211SERPRO1BB1 - 31 - 3
321ILEILE3AA44
421ILEILE3BB44
531PHEVAL1AA5 - 1855 - 185
631PHEVAL1BB5 - 1855 - 185
741THRARG6AA186 - 190186 - 190
841THRARG6BB186 - 190186 - 190
951TRPLEU1AA191 - 267191 - 267
1051TRPLEU1BB191 - 267191 - 267
1161ARGARG3AA268268
1261ARGARG3BB268268
1371LEUHIS1AA269 - 295269 - 295
1471LEUHIS1BB269 - 295269 - 295
1581GLUGLU3AA296296
1681GLUGLU3BB296296
1791LEUGLY1AA297 - 414297 - 414
1891LEUGLY1BB297 - 414297 - 414
19101PHEPHE3AA415415
20101PHEPHE3BB415415
21111ALAALA1AA416 - 465416 - 465
22111ALAALA1BB416 - 465416 - 465
23121ALAALA3AA466466
24121ALAALA3BB466466
25131LEULEU1AA467 - 472467 - 472
26131LEULEU1BB467 - 472467 - 472
27141GLNLYS3AA473 - 474473 - 474
28141GLNLYS3BB473 - 474473 - 474
29151GLUASP1AA475 - 491475 - 491
30151GLUASP1BB475 - 491475 - 491
31161ASPASP3AA492492
32161ASPASP3BB492492
33171ALAARG1AA493 - 556493 - 556
34171ALAARG1BB493 - 556493 - 556
35181GLUGLN6AA557 - 560557 - 560
36181GLUGLN6BB557 - 560557 - 560
37191ALAASP4AA561 - 562561 - 562
38191ALAASP4BB561 - 562561 - 562
39201ARGARG3AA563563
40201ARGARG3BB563563
41211VALSER1AA564 - 716564 - 716
42211VALSER1BB564 - 716564 - 716
43221PLPPLP1AG900
44221PLPPLP1BH900
45231GLCHOH1A - BC - J994 - 3169
46231GLCNO31B - AD - E994 - 1999
112HOHHOH1AI2000 - 2384
212HOHHOH1BJ3170 - 3557

NCS ensembles :
ID
1
2
Detailsthe biological assembly is a homodimer; the homodimer constitutes the asymmetric unit

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Components

#1: Protein Maltodextrin phosphorylase / MALP


Mass: 90547.062 Da / Num. of mol.: 2 / Mutation: H261A, T262F, A263E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EG10560 / Plasmid: PMAP101 / Production host: Escherichia coli (E. coli) / Strain (production host): DELTA MAL518 / References: UniProt: P00490, 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)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#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.: 1145 / 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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Lithium chloride, TRIS (hydroxymethil) aminomethane, maltopentaose, alluminium nitrate, sodium fluoride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.01→111.8 Å / Num. all: 102161 / Num. obs: 100613 / Redundancy: 2.1 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 6.7
Reflection shellResolution: 2.01→2.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2 / Num. unique all: 10682

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L5V

1l5v


Resolution: 2.01→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24387 5058 5 %RANDOM
Rwork0.18998 ---
obs0.1927 95530 86.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---1.15 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.01→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12778 0 150 1145 14073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02113234
X-RAY DIFFRACTIONr_bond_other_d00.0211846
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.94817958
X-RAY DIFFRACTIONr_angle_other_deg3.762327532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5951590
X-RAY DIFFRACTIONr_chiral_restr0.1070.21962
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214658
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022678
X-RAY DIFFRACTIONr_nbd_refined0.220.22814
X-RAY DIFFRACTIONr_nbd_other0.2810.213025
X-RAY DIFFRACTIONr_nbtor_other0.1090.26582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2939
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.216
X-RAY DIFFRACTIONr_mcbond_it0.851.57926
X-RAY DIFFRACTIONr_mcangle_it1.501212710
X-RAY DIFFRACTIONr_scbond_it2.40735308
X-RAY DIFFRACTIONr_scangle_it3.8984.55248
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
110909tight positional0.060.05
2365tight positional0.160.05
122medium positional0.190.5
1235loose positional0.675
110909tight thermal0.270.5
2365tight thermal0.590.5
122medium thermal1.512
1235loose thermal6.1110
LS refinement shellResolution: 2.008→2.06 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 257
Rwork0.27 5175

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