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- PDB-6f2c: Methylglyoxal synthase MgsA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6f2c
TitleMethylglyoxal synthase MgsA from Bacillus subtilis
ComponentsMethylglyoxal synthase
KeywordsLYASE / Methylglyoxal Synthase / PROTEIN BINDING
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / cytosol
Similarity search - Function
Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Rossmann fold ...Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylglyoxal synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsDickmanns, A. / Neumann, P. / Ficner, R.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the regulatory interaction of the methylglyoxal synthase MgsA with the carbon flux regulator Crh inBacillus subtilis.
Authors: Dickmanns, A. / Zschiedrich, C.P. / Arens, J. / Parfentev, I. / Gundlach, J. / Hofele, R. / Neumann, P. / Urlaub, H. / Gorke, B. / Ficner, R. / Stulke, J.
History
DepositionNov 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 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
Item: _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: Methylglyoxal synthase
D: Methylglyoxal synthase
B: Methylglyoxal synthase
F: Methylglyoxal synthase
C: Methylglyoxal synthase
E: Methylglyoxal synthase
H: Methylglyoxal synthase
K: Methylglyoxal synthase
G: Methylglyoxal synthase
I: Methylglyoxal synthase
L: Methylglyoxal synthase
J: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,42640
Polymers210,92412
Non-polymers1,50228
Water9,368520
1
A: Methylglyoxal synthase
D: Methylglyoxal synthase
B: Methylglyoxal synthase
F: Methylglyoxal synthase
C: Methylglyoxal synthase
E: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,39021
Polymers105,4626
Non-polymers92815
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14340 Å2
ΔGint-150 kcal/mol
Surface area26660 Å2
MethodPISA
2
H: Methylglyoxal synthase
K: Methylglyoxal synthase
G: Methylglyoxal synthase
I: Methylglyoxal synthase
L: Methylglyoxal synthase
J: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,03619
Polymers105,4626
Non-polymers57413
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-178 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.930, 109.710, 199.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Methylglyoxal synthase / MGS


Mass: 17576.963 Da / Num. of mol.: 12 / Fragment: residues 3- 610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: mgsA, ypjF, BSU22480 / Plasmid: pGP1301 / Details (production host): Strep-Tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42980, methylglyoxal synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M bicine/Trizma base pH 8.5, 10% w/v PEG 4000, 20% w/v glycerol 30 mM of (0.3 M magnesium chloride, 0.3 M calcium chloride)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.77318 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE, / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77318 Å / Relative weight: 1
ReflectionResolution: 2.339→48.993 Å / Num. obs: 101094 / % possible obs: 99.41 % / Observed criterion σ(I): -3 / Redundancy: 4.728 % / Biso Wilson estimate: 46.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.061 / Χ2: 0.98 / Net I/σ(I): 18.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible allRrim(I) all
2.339-2.4234.7880.65812.41100270.73999.72
2.44-2.544.4960.4363.72100270.86499.50.494
2.54-2.744.9770.2885.83159620.94699.70.323
2.74-3.484.770.09913.79321320.99499.60.111
3.48-3.854.8010.04429.1480730.99899.50.049
3.85-4.224.4350.03137.1654720.99998.60.035
4.22-4.594.8790.02844.7138820.99999.70.031
4.59-144.5340.02545.21132460.99998.70.028
14-174.2540.01958.152320.99999.60.021
17-502.6750.02142.643050.99994.70.026
48.993-50

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XW6

2xw6


Resolution: 2.34→48.993 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 5056 5 %thin shells
Rwork0.1707 ---
obs0.1725 101068 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.1 Å2 / Biso mean: 54.6237 Å2 / Biso min: 15.03 Å2
Refinement stepCycle: final / Resolution: 2.34→48.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 0 77 529 11856
Biso mean--72.98 53.58 -
Num. residues----1468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3391-2.36570.2931670.255631543321100
2.3657-2.39350.30031670.251231773344100
2.3935-2.42270.29511680.256531923360100
2.4227-2.45340.34611680.250231863354100
2.4534-2.48560.27091660.22831423308100
2.4856-2.51970.22581660.21453151331799
2.5197-2.55570.25151680.208631973365100
2.5557-2.59380.26181670.20943181334899
2.5938-2.63440.26321660.20233146331299
2.6344-2.67760.24681670.198931903357100
2.6776-2.72370.20921680.19831963364100
2.7237-2.77320.26121680.187431943362100
2.7732-2.82660.24761670.192131623329100
2.8266-2.88430.23711690.198232133382100
2.8843-2.9470.25171670.19443175334299
2.947-3.01550.26631680.196731853353100
3.0155-3.09090.2371650.20473160332599
3.0909-3.17450.221690.185332073376100
3.1745-3.26790.24871690.189331953364100
3.2679-3.37330.19361700.180332343404100
3.3733-3.49390.22211660.17473165333199
3.4939-3.63370.21121710.16932293400100
3.6337-3.7990.21690.16063213338299
3.799-3.99920.17791670.14713173334098
3.9992-4.24970.18311690.12593206337599
4.2497-4.57760.14811710.122732533424100
4.5776-5.03780.1491710.133732423413100
5.0378-5.76580.151690.14223236340598
5.7658-7.26050.22151730.17793282345599
7.2605-49.00420.20621800.17753376355697
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)
12.55260.6068-0.0762.56260.17792.94510.12370.29010.0823-0.1372-0.11960.326-0.1583-0.35810.00010.42950.0870.06060.3831-0.06540.4283-12.9395-1.2532-71.4953
22.3497-1.09480.2353.29860.12162.7960.0772-0.25090.04930.452-0.10360.5576-0.2988-0.45930.0250.4994-0.00710.17780.3653-0.04680.4255-13.7477-0.2513-47.9555
31.78950.3788-0.51863.5356-0.62481.7191-0.0095-0.1882-0.19820.3554-0.05130.02970.0224-0.06870.06040.4972-0.050.08680.3379-0.00140.41785.3886-21.9243-45.2948
42.94760.73960.33712.20960.67893.79970.1296-0.37590.09220.474-0.1033-0.3085-0.11830.3542-0.00880.5315-0.09040.01160.4077-0.00480.42123.0464-6.3669-42.8648
52.7547-1.097-1.48451.38980.45593.04340.20320.1390.0072-0.1144-0.0932-0.1331-0.1420.1796-0.12510.4104-0.0390.07790.3261-0.03260.387425.5709-3.6637-71.5904
62.1954-0.20980.1123.6273-0.0131.83840.19450.15510.4101-0.2467-0.0772-0.1417-0.5760.1253-0.12740.59570.00210.170.327-0.00520.419711.355615.2388-71.6234
71.77761.15020.16891.3970.51113.22220.018-0.08930.10640.00020.01490.063-0.264-0.0384-0.06210.30320.0780.01890.3749-0.02240.37280.2111-13.9491-94.7389
83.2945-0.6910.24762.72840.20313.43720.07940.42930.3923-0.3711-0.02860.0643-0.6786-0.1144-0.06530.49120.09750.02270.47810.06750.37410.0841-9.6387-117.9651
92.9681-0.0735-0.08092.50410.16771.56340.00630.4343-0.1904-0.4263-0.0269-0.3750.03290.32260.0220.43570.09190.07360.612-0.05640.394918.3998-31.5958-123.4358
102.53710.83960.35921.2737-0.37363.6780.09890.5629-0.447-0.41050.0119-0.06130.3345-0.0325-0.11060.44680.1185-0.04040.5453-0.16170.45370.3737-46.3447-127.7939
112.6397-0.7070.22812.9906-0.12943.47850.104-0.185-0.54750.09690.0158-0.14780.57940.0804-0.10750.40610.0476-0.08950.41020.01880.5218-3.1871-51.5256-99.5841
122.90640.151-0.60511.70970.65891.64850.0712-0.0393-0.11510.0138-0.09320.19670.0784-0.42780.00420.27080.0112-0.04560.4938-0.00560.3565-19.7416-34.7645-97.6762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A-2 - 121
2X-RAY DIFFRACTION2chain 'B'B-1 - 120
3X-RAY DIFFRACTION3chain 'C'C-1 - 120
4X-RAY DIFFRACTION4chain 'D'D-1 - 120
5X-RAY DIFFRACTION5chain 'E'E-1 - 120
6X-RAY DIFFRACTION6chain 'F'F-1 - 120
7X-RAY DIFFRACTION7chain 'G'G-1 - 121
8X-RAY DIFFRACTION8chain 'H'H-1 - 120
9X-RAY DIFFRACTION9chain 'I'I-2 - 120
10X-RAY DIFFRACTION10chain 'J'J-1 - 120
11X-RAY DIFFRACTION11chain 'K'K-1 - 120
12X-RAY DIFFRACTION12chain 'L'L-1 - 120

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