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Basic information

Entry
Database: PDB / ID: 2asv
TitleX-Ray studies on protein complexes: Enzymatic catalysis in Crystals of E. coli Maltodextrin Phosphorylase (MalP)
ComponentsMaltodextrin phosphorylase
KeywordsTRANSFERASE / maltopentaose / carbohydrate recognition / phosphorylase mechanism / ternary oligosaccharide complexes / diffusion of substrates in the crystal / catalysis in the crystal
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 / cytosol / 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
1,5-anhydro-D-glucitol / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGeremia, S. / Campagnolo, M.
CitationJournal: TO BE PUBLISHED
Title: X-Ray studies on protein complexes: Enzymatic catalysis in Crystals of E.coli Maltodextrin Phosphorylase (MalP)
Authors: Geremia, S. / Campagnolo, M.
History
DepositionAug 24, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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.occupancy / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)183,76410
Polymers181,0942
Non-polymers2,6708
Water21,3301184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint1 kcal/mol
Surface area54950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.327, 104.723, 214.787
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
491A
501B
511A
521B
531A
541B
551A
561B
571A
581B
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
321ILEILE2AA44
421ILEILE2BB44
531PHEASN1AA5 - 1725 - 172
631PHEASN1BB5 - 1725 - 172
741GLUGLU3AA173173
841GLUGLU3BB173173
951ALAGLY1AA174 - 236174 - 236
1051ALAGLY1BB174 - 236174 - 236
1161ASPASP3AA237237
1261ASPASP3BB237237
1371PHEPHE1AA238 - 262238 - 262
1471PHEPHE1BB238 - 262238 - 262
1581GLUGLU3AA263263
1681GLUGLU3BB263263
1791GLYLEU1AA264 - 269264 - 269
1891GLYLEU1BB264 - 269264 - 269
19101METMET3AA270270
20101METMET3BB270270
21111GLNLEU1AA271 - 294271 - 294
22111GLNLEU1BB271 - 294271 - 294
23121HISLEU3AA295 - 297295 - 297
24121HISLEU3BB295 - 297295 - 297
25131ALAHIS1AA298 - 325298 - 325
26131ALAHIS1BB298 - 325298 - 325
27141GLNGLN3AA326326
28141GLNGLN3BB326326
29151METASP1AA327 - 469327 - 469
30151METASP1BB327 - 469327 - 469
31161LYSLYS3AA470470
32161LYSLYS3BB470470
33171SERLEU1AA471 - 472471 - 472
34171SERLEU1BB471 - 472471 - 472
35181GLNGLN3AA473473
36181GLNGLN3BB473473
37191LYSPRO1AA474 - 599474 - 599
38191LYSPRO1BB474 - 599474 - 599
39201LEULEU3AA600600
40201LEULEU3BB600600
41211VALSER1AA601 - 716601 - 716
42211VALSER1BB601 - 716601 - 716
43221ASPASP3AA717717
44221ASPASP3BB717717
45231GLYVAL1AA718 - 740718 - 740
46231GLYVAL1BB718 - 740718 - 740
47241METMET3AA741741
48241METMET3BB741741
49251ALAGLY1AA742 - 776742 - 776
50251ALAGLY1BB742 - 776742 - 776
51261METMET3AA777777
52261METMET3BB777777
53271PHEARG1AA778 - 790778 - 790
54271PHEARG1BB778 - 790778 - 790
55281PLPPLP1AI900
56281PLPPLP1BJ900
57291GLCPO44AC - G993 - 999
58291GLCPO44BE - H993 - 1999
112HOHHOH1AK1999 - 2435
212HOHHOH1BL3025 - 3464

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

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Components

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Protein , 1 types, 2 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

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Sugars , 2 types, 4 molecules

#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: Sugar ChemComp-ASO / 1,5-anhydro-D-glucitol / 1,5-ANHYDROSORBITOL


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
D-1-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 1188 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1184 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, lithium chloride, (hydroxymethyl) aminomethane, maltopentaose, 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: CCD / Date: Mar 31, 2004 / 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: 1.95→15 Å / Num. all: 121744 / Num. obs: 119849 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.8 / Num. unique all: 16075 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1L5V

1l5v


Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22604 6018 5 %RANDOM
Rwork0.17939 ---
obs0.18168 113766 97.46 %-
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: 30.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---1 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12778 0 174 1184 14136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02113258
X-RAY DIFFRACTIONr_bond_other_d00.0211860
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9517994
X-RAY DIFFRACTIONr_angle_other_deg3.679327570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44251590
X-RAY DIFFRACTIONr_chiral_restr0.1050.21970
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214650
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022678
X-RAY DIFFRACTIONr_nbd_refined0.2250.23147
X-RAY DIFFRACTIONr_nbd_other0.2860.214188
X-RAY DIFFRACTIONr_nbtor_other0.110.26761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.216
X-RAY DIFFRACTIONr_mcbond_it0.881.57920
X-RAY DIFFRACTIONr_mcangle_it1.568212710
X-RAY DIFFRACTIONr_scbond_it2.53435338
X-RAY DIFFRACTIONr_scangle_it4.0994.55284
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
112029tight positional0.060.05
2441tight positional0.150.05
1127medium positional0.380.5
1139loose positional0.975
112029tight thermal0.290.5
2441tight thermal0.60.5
1127medium thermal1.252
1139loose thermal3.410
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.301 384
Rwork0.258 7168
obs-7680

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