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- PDB-4u3c: Docking Site of Maltohexaose in the Mtb GlgE -

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Basic information

Entry
Database: PDB / ID: 4u3c
TitleDocking Site of Maltohexaose in the Mtb GlgE
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
KeywordsTRANSFERASE / Docking Complex Maltohexaose Maltosyl Transferase
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / alpha-maltohexaose / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.98 Å
AuthorsRonning, D.R. / Lindenberger, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 United States
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors.
Authors: Lindenberger, J.J. / Kumar Veleti, S. / Wilson, B.N. / Sucheck, S.J. / Ronning, D.R.
History
DepositionJul 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: 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: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
B: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
C: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
D: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
E: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
F: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)495,03918
Polymers487,0406
Non-polymers7,99912
Water0
1
A: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
B: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0136
Polymers162,3472
Non-polymers2,6664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-18 kcal/mol
Surface area54190 Å2
MethodPISA
2
C: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
D: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0136
Polymers162,3472
Non-polymers2,6664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-19 kcal/mol
Surface area54520 Å2
MethodPISA
3
E: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules

E: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0136
Polymers162,3472
Non-polymers2,6664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5460 Å2
ΔGint-18 kcal/mol
Surface area54280 Å2
MethodPISA
4
F: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules

F: Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0136
Polymers162,3472
Non-polymers2,6664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5500 Å2
ΔGint-20 kcal/mol
Surface area54170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)338.422, 239.418, 239.447
Angle α, β, γ (deg.)90.000, 134.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-29-

CYS

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Components

#1: Protein
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / GMPMT / (1->4)-alpha-D-glucan:maltose-1-phosphate alpha-D-maltosyltransferase / (1->4)-alpha-D- ...GMPMT / (1->4)-alpha-D-glucan:maltose-1-phosphate alpha-D-maltosyltransferase / (1->4)-alpha-D-glucan:phosphate alpha-D-maltosyltransferase


Mass: 81173.352 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: glgE, MT1369 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WQ16, starch synthase (maltosyl-transferring)
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltohexaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 990.860 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltohexaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE

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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: 7.05 Å3/Da / Density % sol: 82.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5 and 1.0 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.98→50 Å / Num. obs: 122284 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 116.73 Å2 / Net I/σ(I): 13.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data collection
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 3.98→43.725 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 5670 5.02 %
Rwork0.2235 107284 -
obs0.2252 112954 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.5 Å2 / Biso mean: 121.6738 Å2 / Biso min: 74.64 Å2
Refinement stepCycle: final / Resolution: 3.98→43.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31398 0 540 0 31938
Biso mean--129.92 --
Num. residues----3960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832956
X-RAY DIFFRACTIONf_angle_d1.65445131
X-RAY DIFFRACTIONf_chiral_restr0.074968
X-RAY DIFFRACTIONf_plane_restr0.015832
X-RAY DIFFRACTIONf_dihedral_angle_d15.40211657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9804-4.02560.2757990.28431863196252
4.0256-4.07290.29911710.2843670384198
4.0729-4.12250.31041850.28363549373499
4.1225-4.17470.32061880.26913600378899
4.1747-4.22960.26491730.2753659383299
4.2296-4.28750.22531790.27743565374499
4.2875-4.34870.33582060.26833620382699
4.3487-4.41350.28991880.26473651383999
4.4135-4.48240.29532020.25933525372799
4.4824-4.55580.20821860.258236223808100
4.5558-4.63430.2921910.254536333824100
4.6343-4.71850.31661940.246737043898100
4.7185-4.80910.29221930.236435823775100
4.8091-4.90720.3421990.235636663865100
4.9072-5.01370.2531930.22336313824100
5.0137-5.13020.2891880.228436483836100
5.1302-5.25830.26382010.229735843785100
5.2583-5.40020.24551940.244336983892100
5.4002-5.55880.28322040.231336453849100
5.5588-5.73780.24522040.244737073911100
5.7378-5.94240.33541770.238236483825100
5.9424-6.17970.29571680.247936403808100
6.1797-6.46010.24182060.23636673873100
6.4601-6.79950.27171920.226436093801100
6.7995-7.22380.28992010.220437093910100
7.2238-7.77860.28352080.210736753883100
7.7786-8.55620.1951850.189336373822100
8.5562-9.78220.18131820.155836933875100
9.7822-12.27910.16992040.1333643384799
12.2791-43.7280.21412090.21133541375095

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