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- PDB-2azd: X-Ray studies on Maltodextrin Phosphorylase (MalP) Complexes: rec... -

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Basic information

Entry
Database: PDB / ID: 2azd
TitleX-Ray studies on Maltodextrin Phosphorylase (MalP) Complexes: recognition of substrates and CATALYTIC 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
PYRIDOXAL-5'-PHOSPHATE / VANADATE ION / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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
DepositionSep 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)183,39610
Polymers181,0942
Non-polymers2,3028
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint15 kcal/mol
Surface area57830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.779, 105.892, 220.230
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
471A
481B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERPRO1AA1 - 31 - 3
21SERPRO1BB1 - 31 - 3
32PROILE3AA3 - 43 - 4
42PROILE3BB3 - 43 - 4
53PHEVAL1AA5 - 1855 - 185
63PHEVAL1BB5 - 1855 - 185
74THRARG6AA186 - 190186 - 190
84THRARG6BB186 - 190186 - 190
95TRPLEU1AA191 - 267191 - 267
105TRPLEU1BB191 - 267191 - 267
116ARGARG3AA268268
126ARGARG3BB268268
137LEUHIS1AA269 - 295269 - 295
147LEUHIS1BB269 - 295269 - 295
158GLUGLU3AA296296
168GLUGLU3BB296296
179LEUGLY1AA297 - 414297 - 414
189LEUGLY1BB297 - 414297 - 414
1910PHEPHE3AA415415
2010PHEPHE3BB415415
2111ALAALA1AA416 - 465416 - 465
2211ALAALA1BB416 - 465416 - 465
2312ALAALA3AA466466
2412ALAALA3BB466466
2513LEULEU1AA467 - 472467 - 472
2613LEULEU1BB467 - 472467 - 472
2714GLNLYS3AA473 - 474473 - 474
2814GLNLYS3BB473 - 474473 - 474
2915GLUASP1AA475 - 491475 - 491
3015GLUASP1BB475 - 491475 - 491
3116ASPASP3AA492492
3216ASPASP3BB492492
3317ALAARG1AA493 - 556493 - 556
3417ALAARG1BB493 - 556493 - 556
3518GLUGLN6AA557 - 560557 - 560
3618GLUGLN6BB557 - 560557 - 560
3719ALAASP1AA561 - 562561 - 562
3819ALAASP1BB561 - 562561 - 562
3920ARGARG3AA563563
4020ARGARG3BB563563
4121VALSER1AA564 - 716564 - 716
4221VALSER1BB564 - 716564 - 716
4322ASPASP3AA717717
4422ASPASP3BB717717
4523GLYARG1AA718 - 796718 - 796
4623GLYARG1BB718 - 796718 - 796
4724TRSVO41AH - E990 - 999
4824TRSVO41BJ - F1990 - 1999
Detailsthe biological assembly is a homodimer; the homodimer constitutes the asymmetric unit

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Maltodextrin phosphorylase


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)-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

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Non-polymers , 4 types, 638 molecules

#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.5 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, lithium chloride, TRIS (HYDROXYMETHIL)AMINOMETHANE, MALTOPENTAOSE, SODIUM ORTHOVANADATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: CCD
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: 2.16→111.8 Å / Num. all: 96210 / Num. obs: 88911 / Redundancy: 6.5 % / Biso Wilson estimate: 34.35 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 12.6
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.2 / Num. unique all: 12410

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→6.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.054 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24967 4458 5 %RANDOM
Rwork0.20468 ---
obs0.207 84393 91.54 %-
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: 35.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.16→6.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12778 0 146 632 13556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02113228
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211844
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.94717944
X-RAY DIFFRACTIONr_angle_other_deg1.187327532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97951590
X-RAY DIFFRACTIONr_chiral_restr0.1160.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214650
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022678
X-RAY DIFFRACTIONr_nbd_refined0.2250.22792
X-RAY DIFFRACTIONr_nbd_other0.2550.213142
X-RAY DIFFRACTIONr_nbtor_other0.0940.27180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2552
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.24
X-RAY DIFFRACTIONr_mcbond_it1.0031.57928
X-RAY DIFFRACTIONr_mcangle_it1.787212722
X-RAY DIFFRACTIONr_scbond_it2.59835300
X-RAY DIFFRACTIONr_scangle_it4.1634.55222
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
12126tight positional0.080.05
250loose positional0.925
12126tight thermal0.290.5
250loose thermal5.5110
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 318
Rwork0.279 5931

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