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- PDB-4u33: Structure of Mtb GlgE bound to maltose -

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Basic information

Entry
Database: PDB / ID: 4u33
TitleStructure of Mtb GlgE bound to maltose
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
KeywordsTRANSFERASE / Complex Wild-type Maltose 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-1,4-glucan:maltose-1-phosphate maltosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.293 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 18, 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 / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _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)489,09412
Polymers487,0406
Non-polymers2,0546
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)163,0314
Polymers162,3472
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-16 kcal/mol
Surface area52150 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)163,0314
Polymers162,3472
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-15 kcal/mol
Surface area52360 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)163,0314
Polymers162,3472
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4740 Å2
ΔGint-16 kcal/mol
Surface area52800 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)163,0314
Polymers162,3472
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4710 Å2
ΔGint-17 kcal/mol
Surface area52280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)343.231, 242.601, 243.672
Angle α, β, γ (deg.)90.000, 135.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-29-

CYS

21F-29-

CYS

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA15 - 702
211chain BB15 - 699
311chain CC15 - 699
411chain DD15 - 699
511chain EE15 - 699
611chain FF15 - 699

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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

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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: 7.35 Å3/Da / Density % sol: 83.26 %
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-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 210465 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 88.1 Å2 / Net I/σ(I): 15

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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: 3.293→47.638 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 10495 5 %
Rwork0.1937 199279 -
obs0.1952 209774 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.97 Å2 / Biso mean: 71.0353 Å2 / Biso min: 39.28 Å2
Refinement stepCycle: final / Resolution: 3.293→47.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31458 0 138 0 31596
Biso mean--82.14 --
Num. residues----3966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01632590
X-RAY DIFFRACTIONf_angle_d1.41544578
X-RAY DIFFRACTIONf_chiral_restr0.0784794
X-RAY DIFFRACTIONf_plane_restr0.0095844
X-RAY DIFFRACTIONf_dihedral_angle_d16.38411674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18752X-RAY DIFFRACTION14.783TORSIONAL
12B18752X-RAY DIFFRACTION14.783TORSIONAL
13C18752X-RAY DIFFRACTION14.783TORSIONAL
14D18752X-RAY DIFFRACTION14.783TORSIONAL
15E18752X-RAY DIFFRACTION14.783TORSIONAL
16F18752X-RAY DIFFRACTION14.783TORSIONAL
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 (%)
3.2928-3.33020.41492800.32875455573581
3.3302-3.36930.32873560.325166256981100
3.3693-3.41040.38243490.308466937042100
3.4104-3.45360.29633580.28166907048100
3.4536-3.4990.2853510.253466927043100
3.499-3.54690.26453560.268166126968100
3.5469-3.59760.27983410.265566987039100
3.5976-3.65120.27453480.269366967044100
3.6512-3.70830.27133540.25566426996100
3.7083-3.76910.22623600.2667257085100
3.7691-3.8340.29413560.244467077063100
3.834-3.90370.25723490.236266506999100
3.9037-3.97870.27563510.219766837034100
3.9787-4.05990.2053710.20626595696699
4.0599-4.14820.21763550.20056640699599
4.1482-4.24460.26053420.19846683702599
4.2446-4.35070.23263250.18926699702499
4.3507-4.46820.19093370.17367217058100
4.4682-4.59960.18443480.172366256973100
4.5996-4.74790.22323490.16856692704199
4.7479-4.91750.16273510.163166877038100
4.9175-5.11410.19973440.156367047048100
5.1141-5.34660.17053550.164866807035100
5.3466-5.62810.22493320.178167357067100
5.6281-5.980.22033600.179867207080100
5.98-6.44070.19523330.176967397072100
6.4407-7.0870.20933710.172267297100100
7.087-8.10820.18533600.15767727132100
8.1082-10.19890.17423770.13167227099100
10.1989-47.64330.19833760.1676568694496

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