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- PDB-1qm5: Phosphorylase recognition and phosphorylysis of its oligosacchari... -

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Basic information

Entry
Database: PDB / ID: 1qm5
TitlePhosphorylase recognition and phosphorylysis of its oligosaccharide substrate: answers to a long outstanding question
ComponentsMALTODEXTRIN PHOSPHORYLASE
KeywordsPHOSPHORYLASE / THIO-OLIGOSACCHARIDE / PHOSPHOROLYSIS / MALP / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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
alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWatson, K.A. / McCleverty, C. / Geremia, S. / Cottaz, S. / Driguez, H. / Johnson, L.N.
CitationJournal: Embo J. / Year: 1999
Title: Phosphorylase Recognition and Phosphorolysis of its Oligosaccharide Substrate: Answers to a Long Outstanding Question
Authors: Watson, K.A. / Mccleverty, C. / Geremia, S. / Cottaz, S. / Driguez, H. / Johnson, L.N.
History
DepositionSep 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Jul 1, 2020Group: Advisory / Data collection / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.type / _pdbx_nonpoly_scheme.ndb_seq_num
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 / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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 / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: MALTODEXTRIN PHOSPHORYLASE
B: MALTODEXTRIN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,40410
Polymers180,9942
Non-polymers2,4108
Water13,583754
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-28.4 kcal/mol
Surface area67780 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.410, 61.500, 132.380
Angle α, β, γ (deg.)90.00, 105.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999928, -0.011762, 0.002474), (-0.010777, 0.786185, -0.617897), (0.005323, -0.617879, -0.786255)
Vector: -37.4114, 26.2104, 76.2085)
DetailsTHE ASYMMETRIC UNIT CONTAINS THE DIMERIC COMPLEX

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MALTODEXTRIN PHOSPHORYLASE / MALP / ECP


Mass: 90496.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CO-FACTOR PLP (RESID 999) LINKED TO LYS645 (K680 RABBIT MUSCLE NUMBERING)
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cell line: DELTA MALA518 / Cellular location: CYTOPLASM / Plasmid: PMAP101 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DELTA MALA518 / References: UniProt: P00490, glycogen phosphorylase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 4-thio-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...4-thio-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 682.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5_4*S]/1-1-1-2/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-Glcp4SH]{}}}}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.: 2
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, 758 molecules

#3: 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.: 754 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCOVALENT ATTACHMENT OF PYRIDOXAL PHOSPHATE TO LYS 645. THE PDB FILE HAS BEEN LABELED ACCORDING TO ...COVALENT ATTACHMENT OF PYRIDOXAL PHOSPHATE TO LYS 645. THE PDB FILE HAS BEEN LABELED ACCORDING TO THE NUMBERING SYSTEM USED FOR E. COLI MALTODEXTRIN PHOSPHORYLASE.
Sequence detailsTHE SWISSPROT SEQUENCE P00490 (PHSM_ECOLI) IS FROM REFERENCE D.PALM D,R.GOERL,G.WEIDINGER,R.ZEIER,B. ...THE SWISSPROT SEQUENCE P00490 (PHSM_ECOLI) IS FROM REFERENCE D.PALM D,R.GOERL,G.WEIDINGER,R.ZEIER,B.FISCHER,R.SCHINZEL R. E. COLI MALTODEXTRIN PHOSPHORYLASE: PRIMARY STRUCTURE AND DELETION MAPPING OF THE C-TERMINAL SITE. Z. NATURFORSCH. C 42: 394-400 (1987). THE SEQUENCE IN THIS PDB ENTRY MATCHES THAT IN REFERENCE F.R.BLATTNER,G.PLUNKETT III,C.A.BLOCH,N.T.PERNA,V.BURLAND, M.RILEY,J.COLLADO-VIDES,F.D.GLASNER,C.K.RODE,G.F.MAYHEW, J.GREGOR,N.W.DAVIS,H.A.KIRKPATRICK,M.A.GOEDEN,D.J.ROSE, B.MAU,Y.SHAO, THE COMPLETE GENOME SEQUENCE OF ESCHERICHIA COLI K-12 SCIENCE 277: 1453-1474 (1997). (STRAIN=K12 / MG1655) THE CONFLICTS LISTED IN SEQADV RECORDS ARE KNOWN CONFLICTS BETWEEN THE TWO SEQUENCE DETERMINATIONS. SWS 1QM5 CONFLICT 293 293 E -> K CONFLICT 487 487 V -> E CONFLICT 489 489 L -> F CONFLICT 498 498 L -> Q CONFLICT 501 501 V -> E CONFLICT 521 521 D -> E CONFLICT 547 547 H -> R HOWEVER 1QM5 DOES NOT HAVE THESE CONFLICTS CONFLICT 681 681 E -> K CONFLICT 687 687 L -> D CONFLICT 700 700 D -> G

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: (26-32)% PEG 4000, (0.1-0.6)M LICL, 0.1M TRIS/HCL PH8.5, 18 DEG C, HANGING DROP, 10MG/ML PROTEIN, 20MM GSG4, 50MM PHOSPHATE, pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
350 mM1dropNa2HPO4
426-32 %PEG40001reservoir
50.1-0.6 M1reservoirLiCl
61 MTris-HCl1reservoir
2GSG41drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS/WIGGLER
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 72681 / % possible obs: 80 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.1 % / % possible all: 64.5
Reflection
*PLUS
Num. measured all: 152192
Reflection shell
*PLUS
% possible obs: 64.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: STRICT NCS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1450 2 %RANDOM
Rwork0.228 ---
obs0.228 72681 80 %-
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å2-2.06 Å2
2---0.44 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12756 0 152 754 13662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.82
X-RAY DIFFRACTIONx_mcangle_it3.023
X-RAY DIFFRACTIONx_scbond_it2.92
X-RAY DIFFRACTIONx_scangle_it4.713
LS refinement shellResolution: 2→2.1 Å / Total num. of bins used: 10 / % reflection obs: 64.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROPARAM.THIO
X-RAY DIFFRACTION2TOPH19X.PROPARAM_NEW.PLP
X-RAY DIFFRACTION3PROTEIN_REP.PARAMPARAM.PHOSPHATE
X-RAY DIFFRACTION4WATER.PARAM

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