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- PDB-6tvp: Structure of Mycobacterium smegmatis alpha-maltose-1-phosphate sy... -

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Basic information

Entry
Database: PDB / ID: 6tvp
TitleStructure of Mycobacterium smegmatis alpha-maltose-1-phosphate synthase GlgM
ComponentsAlpha-maltose-1-phosphate synthase
KeywordsSUGAR BINDING PROTEIN / GlgM / alpha-maltose-1-phosphate synthase / glycosyltransferase / carbohydrate-active enzymes.
Function / homologyalpha-maltose-1-phosphate synthase / Alpha-maltose-1-phosphate synthase / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycogen biosynthetic process / glycosyltransferase activity / Alpha-maltose-1-phosphate synthase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSyson, K. / Stevenson, C.E.M. / Lawson, D.M. / Bornemann, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J004561/1 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure of the Mycobacterium smegmatis alpha-maltose-1-phosphate synthase GlgM.
Authors: Syson, K. / Stevenson, C.E.M. / Lawson, D.M. / Bornemann, S.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-maltose-1-phosphate synthase
B: Alpha-maltose-1-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1164
Polymers87,0702
Non-polymers462
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Confirmation that GlgM forms a dimer in solution was obtained using size exclusion chromatography. This indicated a molecular mass of 107 kDa, close to the theoretical mass ...Evidence: gel filtration, Confirmation that GlgM forms a dimer in solution was obtained using size exclusion chromatography. This indicated a molecular mass of 107 kDa, close to the theoretical mass of a dimer of 87 kDa; the slight over-estimation of this value could be due to the elongated aspect of the GlgM homodimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-40 kcal/mol
Surface area32760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.371, 144.928, 46.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha-maltose-1-phosphate synthase / M1P synthase / ADP-alpha-D-glucose:alpha-D-glucose-1-phosphate 4-alpha-D-glucosyltransferase / M1P- ...M1P synthase / ADP-alpha-D-glucose:alpha-D-glucose-1-phosphate 4-alpha-D-glucosyltransferase / M1P-producing glucosyltransferase


Mass: 43535.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: glgM, glgA, MSMEG_5080, MSMEI_4954 / Production host: Escherichia coli (E. coli)
References: UniProt: A0R2E2, alpha-maltose-1-phosphate synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 0.2 M malonate and 100 mM Bis-Tris Propane, pH 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.9795
SYNCHROTRONDiamond I0321.0052
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELSep 19, 2016
DECTRIS PILATUS 6M2PIXELAug 1, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.00521
Reflection

Biso Wilson estimate: 31.5 Å2 / Entry-ID: 6TVP

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRrim(I) allDiffraction-IDNet I/σ(I)
1.9-72.467320896.313.310.0880.092118.8
3.5-137.451134510051.10.9980.3820.386212.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
1.9-1.9413.22.1021.444880.522.187195.8
3.5-3.591.4593.98100.871.474299.9

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→72.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.861 / SU ML: 0.098 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 3792 5.2 %RANDOM
Rwork0.1731 ---
obs0.1751 69344 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.95 Å2 / Biso mean: 39.312 Å2 / Biso min: 23.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--1.72 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.9→72.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 2 452 6260
Biso mean--46.56 46.21 -
Num. residues----775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135951
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175491
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6358154
X-RAY DIFFRACTIONr_angle_other_deg1.4061.56512633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24221.077297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32115863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8591547
X-RAY DIFFRACTIONr_chiral_restr0.0770.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021251
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 259 -
Rwork0.295 5080 -
all-5339 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.47130.1261.0814.50490.42061.0388-0.0192-0.11810.396700.00250.1552-0.2799-0.08490.01670.18110.0830.0340.1884-0.03070.0722-9.5332.95940.6586
23.97741.2548-2.94031.9074-2.03654.24210.2066-0.33410.50870.02470.04650.1343-0.43680.0075-0.25310.24940.06660.01990.1858-0.06430.1165-5.213935.58462.3685
33.1578-0.3714-0.32011.9893-0.2481.43630.0327-0.19880.1644-0.1267-0.0289-0.0456-0.1909-0.0254-0.00380.12830.04070.01080.0977-0.00960.0099-0.316225.8221-3.1928
46.480.51570.96180.6654-1.79149.13220.09420.6330.0916-0.20960.11950.25090.0028-0.44-0.21370.25670.0333-0.13090.1307-0.03420.2169-5.958620.0982-17.0003
53.5779-0.3937-0.7192.85862.07934.1426-0.1017-0.2575-0.4612-0.0253-0.01460.3840.0772-0.28230.11620.12560.0473-0.00730.13650.08170.1478-13.470613.436-2.2532
65.40712.5321-3.20877.02511.24423.25410.2401-0.12890.504-0.1929-0.09050.4082-0.42710.0499-0.14960.37760.0694-0.16140.1925-0.0590.1396-31.548837.38461.1434
73.789-1.6492-0.57316.3387-0.64723.7342-0.12630.08870.39270.134-0.00540.0189-0.42520.08420.13170.18970.0425-0.05090.05310.00660.0633-37.577737.5936-14.2495
89.3844-3.17021.76325.8205-0.71614.4696-0.06450.17470.0126-0.1906-0.09180.09420.09120.03570.15630.16230.0229-0.01510.01430.00650.0296-37.115125.1732-20.4021
96.3069-0.6642-0.89272.50910.75393.3271-0.06710.12660.0259-0.2602-0.0713-0.1019-0.23530.21630.13840.19570.0628-0.01080.06350.02730.0592-34.127132.8987-23.8072
101.4067-0.44540.47593.55020.66542.5201-0.0949-0.1005-0.06610.03690.06090.0423-0.10790.19120.0340.08710.04950.00760.06310.01880.0337-35.292624.4915-9.0995
1111.01722.79261.76043.60071.45544.0342-0.0227-0.8302-0.23540.31940.01140.22030.1085-0.04250.01140.17580.09670.04920.20320.02560.0405-34.985726.78684.6196
1211.6956-7.19020.083210.9749-0.5792.82490.1444-0.5025-0.87290.3221-0.2390.7540.214-0.10740.09460.1673-0.01080.03730.3137-0.01390.1003-13.241320.343211.1892
133.5154-0.4457-0.73934.47340.86032.08490.0513-0.01060.0526-0.0682-0.0316-0.2085-0.118-0.0292-0.01960.1286-0.0440.01860.01970.00190.038224.60824.1821-18.7165
142.8118-0.05091.16391.4122-0.32319.31-0.0126-0.31290.17590.1506-0.0689-0.0842-0.2495-0.03370.08150.1362-0.02150.00330.1026-0.03020.119913.619927.8967-8.5742
154.1795-0.71720.03381.79550.60552.60730.02070.1166-0.0908-0.022-0.06410.0316-0.158-0.09050.04340.1071-0.03420.00580.0233-0.00780.003514.170617.8542-16.7421
161.8421-1.37621.43645.124.88269.7963-0.1014-0.06340.25050.25790.1679-0.35690.21160.1561-0.06650.2734-0.00270.00860.30620.01050.236519.742311.28574.4848
171.4814-1.0039-1.52391.8821.38473.7294-0.0333-0.1487-0.25390.15620.0208-0.05340.3082-0.30010.01250.1105-0.0598-0.01190.11030.07610.113813.808411.7466-8.857
189.5313-4.8349-5.86387.23445.19284.66210.1997-0.2613-0.66210.8372-0.50850.16010.3976-0.13250.30880.5246-0.1302-0.0080.0940.02390.233216.8431.2955-9.7931
199.61632.44180.06252.35280.54811.8775-0.1331-0.0834-0.1277-0.1550.0241-0.06760.0296-0.02340.1090.2331-0.02520.00890.0049-0.00480.141625.94196.4862-19.0705
200.99610.57161.06540.5492-0.17533.9444-0.2630.1830.0639-0.1183-0.1933-0.0874-0.44631.26420.45630.5353-0.0203-0.03520.5495-0.06630.911957.415713.6766-15.6414
210.9827-0.5938-1.15842.24610.61925.16240.0802-0.24060.25260.14950.0515-0.4957-0.31070.534-0.13170.2307-0.028-0.10820.225-0.13920.555450.63343.6161.3559
221.5887-0.64110.48240.49471.110411.7982-0.1794-0.47160.0780.14270.1501-0.0983-0.89340.16610.02930.4054-0.1122-0.03270.2218-0.04040.622850.412515.3174-8.534
231.795-0.2907-0.16623.3457-1.28433.4564-0.0589-0.06240.3018-0.0510.0341-0.5398-0.18080.10660.02480.12090.00980.01430.0368-0.07720.31743.1001-2.7737-11.4872
2411.8142-1.72411.73313.41030.5123.24340.10550.7231-0.6064-0.3283-0.1323-0.0980.34840.02850.02680.2246-0.0040.05590.0501-0.02630.103824.33038.7011-27.1962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 23
2X-RAY DIFFRACTION2A24 - 56
3X-RAY DIFFRACTION3A57 - 112
4X-RAY DIFFRACTION4A113 - 137
5X-RAY DIFFRACTION5A138 - 171
6X-RAY DIFFRACTION6A172 - 184
7X-RAY DIFFRACTION7A185 - 209
8X-RAY DIFFRACTION8A210 - 227
9X-RAY DIFFRACTION9A228 - 265
10X-RAY DIFFRACTION10A266 - 354
11X-RAY DIFFRACTION11A355 - 371
12X-RAY DIFFRACTION12A372 - 387
13X-RAY DIFFRACTION13B-1 - 56
14X-RAY DIFFRACTION14B57 - 76
15X-RAY DIFFRACTION15B77 - 112
16X-RAY DIFFRACTION16B113 - 122
17X-RAY DIFFRACTION17B123 - 148
18X-RAY DIFFRACTION18B149 - 159
19X-RAY DIFFRACTION19B160 - 178
20X-RAY DIFFRACTION20B179 - 192
21X-RAY DIFFRACTION21B193 - 263
22X-RAY DIFFRACTION22B264 - 275
23X-RAY DIFFRACTION23B276 - 367
24X-RAY DIFFRACTION24B368 - 387

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