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- PDB-5cj5: Structure of Mycobacterium thermoresistibile GlgE APO form at 3.1... -

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Basic information

Entry
Database: PDB / ID: 5cj5
TitleStructure of Mycobacterium thermoresistibile GlgE APO form at 3.13A resolution
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase
KeywordsTRANSFERASE / GlgE / Maltose / GH13 / maltosyltransferase
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / GLGE, C-terminal / 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 / Glycosyl hydrolase, all-beta ...: / GLGE, C-terminal / 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 / 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-1,4-glucan:maltose-1-phosphate maltosyltransferase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.13 Å
AuthorsMendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L.
CitationJournal: Sci Rep / Year: 2015
Title: Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism.
Authors: Mendes, V. / Blaszczyk, M. / Maranha, A. / Empadinhas, N. / Blundell, T.L.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)155,2362
Polymers155,2362
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-15 kcal/mol
Surface area55780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.639, 197.639, 105.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 0 - 696 / Label seq-ID: 2 - 698

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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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


Mass: 77618.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria)
Gene: glgE, KEK_12948 / Production host: Escherichia coli (E. coli)
References: UniProt: G7CL00, starch synthase (maltosyl-transferring)

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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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Bicine pH9.5, Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 3.13→171.16 Å / Num. all: 41628 / Num. obs: 41628 / % possible obs: 100 % / Redundancy: 13.5 % / Rpim(I) all: 0.063 / Rrim(I) all: 0.234 / Rsym value: 0.218 / Net I/av σ(I): 3.268 / Net I/σ(I): 13 / Num. measured all: 563635
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs
3.13-3.313.61.5410.58293460760.4471.5412.3
3.3-3.513.20.9690.87506956920.2880.9693.7
3.5-3.7413.70.5931.27378153760.1720.5936.3
3.74-4.0413.60.3821.96814950170.1110.3829.2
4.04-4.4313.70.233.26307945960.0670.2314.2
4.43-4.9513.60.1594.75702641930.0460.15918.8
4.95-5.7113.70.1395.35068436980.040.13920.6
5.71-713.50.1186.24255231510.0340.11822.7
7-9.913.40.0729.33277124490.0210.07232.5
9.9-171.1612.70.06101759013800.0170.0638.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.13 Å171.16 Å
Translation3.13 Å171.16 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CGM

5cgm


Resolution: 3.13→171.16 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.63 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3083 2093 5.03 %Random selection
Rwork0.2587 39519 --
obs0.2649 41621 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.41 Å2 / Biso mean: 73.8803 Å2 / Biso min: 22.86 Å2
Refinement stepCycle: final / Resolution: 3.13→171.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10448 0 0 0 10448
Num. residues----1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310822
X-RAY DIFFRACTIONf_angle_d1.83214795
X-RAY DIFFRACTIONf_chiral_restr0.081561
X-RAY DIFFRACTIONf_plane_restr0.0111968
X-RAY DIFFRACTIONf_dihedral_angle_d19.2073930
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5471X-RAY DIFFRACTION17.62TORSIONAL
12B5471X-RAY DIFFRACTION17.62TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1298-3.20260.34541520.30712653280595
3.2026-3.28270.38251300.29762589271995
3.2827-3.37140.35051640.2952566273094
3.3714-3.47060.32981350.28912627276295
3.4706-3.58260.35831170.27712639275696
3.5826-3.71070.29951390.26532641278095
3.7107-3.85920.31361490.26872623277295
3.8592-4.03480.32521430.26412608275195
4.0348-4.24740.26871340.24512636277095
4.2474-4.51350.29411380.25352617275595
4.5135-4.86180.29461310.2482645277695
4.8618-5.35070.27721370.24282652278995
5.3507-6.12420.29431400.24762636277695
6.1242-7.71280.29451550.26542655281094
7.7128-57.06290.33231290.25692732286195

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