[English] 日本語
Yorodumi
- PDB-2aw3: X-Ray studies on maltodextrin phosphorylase complexes: recognitio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aw3
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 / 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
PYRIDOXAL-5'-PHOSPHATE / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 13, 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 2.1Oct 25, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)183,4388
Polymers181,0942
Non-polymers2,3446
Water20,9331162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-28 kcal/mol
Surface area56670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.297, 105.887, 219.520
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

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERASP1AA1 - 1001 - 100
21SERASP1BB1 - 1001 - 100
32LEULEU2AA101101
42LEULEU2BB101101
53LEUGLY1AA102 - 114102 - 114
63LEUGLY1BB102 - 114102 - 114
74LEULEU2AA115115
84LEULEU2BB115115
95GLYLYS1AA116 - 184116 - 184
105GLYLYS1BB116 - 184116 - 184
116VALTRP5AA185 - 191185 - 191
126VALTRP5BB185 - 191185 - 191
137GLULEU1AA192 - 267192 - 267
147GLULEU1BB192 - 267192 - 267
158ARGARG2AA268268
168ARGARG2BB268268
179LEUHIS1AA269 - 295269 - 295
189LEUHIS1BB269 - 295269 - 295
1910GLUGLU2AA296296
2010GLUGLU2BB296296
2111LEUASN1AA297 - 372297 - 372
2211LEUASN1BB297 - 372297 - 372
2312GLUGLU2AA373373
2412GLUGLU2BB373373
2513ILELYS1AA374 - 503374 - 503
2613ILELYS1BB374 - 503374 - 503
2714GLNGLN2AA504504
2814GLNGLN2BB504504
2915ALAARG1AA505 - 556505 - 556
3015ALAARG1BB505 - 556505 - 556
3116GLUALA5AA557 - 561557 - 561
3216GLUALA5BB557 - 561557 - 561
3317ASPSER1AA562 - 716562 - 716
3417ASPSER1BB562 - 716562 - 716
3518ASPASP2AA717717
3618ASPASP2BB717717
3719GLYPLP1AA - G718 - 900718
3819GLYPLP1BB - H718 - 900718
3920BGCGLC1AC994 - 998
4020BGCGLC1BD994 - 998

-
Components

#1: Protein Maltodextrin phosphorylase / MalP


Mass: 90547.062 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 1162 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ELECTRON DENSITY MAPS AGREE WITH A DIFFERENT ASSIGNMENT OF THESE THREE CONTIGUOUS AMINO ACIDS ...THE ELECTRON DENSITY MAPS AGREE WITH A DIFFERENT ASSIGNMENT OF THESE THREE CONTIGUOUS AMINO ACIDS THAN IN THE SEQUENCE DATABASE MATCH: ALA261 PHE262 GLU263 INSTEAD OF HIS, THR, ALA.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, LITHIUM CHLORIDE, TRIS(HYDROXYMETHIL) AMINOMETHANE, MALTOPENTAOSE, LITHIUM SULPHATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
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: 2.2→111.8 Å / Num. all: 90262 / Num. obs: 88185 / Redundancy: 4.6 % / Biso Wilson estimate: 28.96 Å2 / Rmerge(I) obs: 0.252 / Net I/σ(I): 7.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.9 / Num. unique all: 12149

-
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: 2.2→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.7 / SU ML: 0.164 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23598 4396 5 %RANDOM
Rwork0.1755 ---
obs0.17848 83713 98.02 %-
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: 28.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12778 0 152 1162 14092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02113238
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211846
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.94817964
X-RAY DIFFRACTIONr_angle_other_deg1.113327532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75851590
X-RAY DIFFRACTIONr_chiral_restr0.1260.21962
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214650
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022678
X-RAY DIFFRACTIONr_nbd_refined0.2170.22774
X-RAY DIFFRACTIONr_nbd_other0.2580.213416
X-RAY DIFFRACTIONr_nbtor_other0.0920.27288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2926
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.215
X-RAY DIFFRACTIONr_mcbond_it0.8971.57920
X-RAY DIFFRACTIONr_mcangle_it1.667212710
X-RAY DIFFRACTIONr_scbond_it2.64935318
X-RAY DIFFRACTIONr_scangle_it4.414.55254
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
12125tight positional0.060.05
147medium positional0.860.5
111loose positional1.135
12125tight thermal0.270.5
147medium thermal3.052
111loose thermal4.5210
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 274
Rwork0.248 5856

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more