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- PDB-8u2v: Crystal Structure of methylglyoxal synthase from Borrelia burgdorferi -

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Basic information

Entry
Database: PDB / ID: 8u2v
TitleCrystal Structure of methylglyoxal synthase from Borrelia burgdorferi
ComponentsMethylglyoxal synthase
KeywordsLYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / methylglyoxal
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity
Similarity search - Function
Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain
Similarity search - Domain/homology
BROMIDE ION / Methylglyoxal synthase
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of methylglyoxal synthase from Borrelia burgdorferi
Authors: Lovell, S. / Liu, L. / Cooper, A. / Buchko, G.W. / Battaile, K.P.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylglyoxal synthase
B: Methylglyoxal synthase
C: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0886
Polymers48,8493
Non-polymers2403
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.866, 110.866, 91.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Methylglyoxal synthase /


Mass: 16282.855 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: mgsA / Plasmid: BobuA.00692.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O51339
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus Fusion D7: 20% (v/v) Ethylene glycol; 10% (w/v) PEG 8000, 0.05M Tris (base); 0.05M BICINE pH 8.5, 0.01M Sodium fluoride, 0.01M Sodium bromide, 0.01M Sodium iodide, 0.2 M xylitol, 0. ...Details: Morpheus Fusion D7: 20% (v/v) Ethylene glycol; 10% (w/v) PEG 8000, 0.05M Tris (base); 0.05M BICINE pH 8.5, 0.01M Sodium fluoride, 0.01M Sodium bromide, 0.01M Sodium iodide, 0.2 M xylitol, 0.02 M D-{-)-fructose, 0.02 M D-sorbitol, 0.02 M myo-inositol, 0.02 M L-rhamnose monohydrate. BobuA.00692.a.A1.PB00123 at 15 mg/mL. plate 13451 well D7 drop1. Puck: PSL-0612, Cryo: direct.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→49.58 Å / Num. obs: 20304 / % possible obs: 100 % / Redundancy: 23.8 % / CC1/2: 1 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.032 / Rrim(I) all: 0.153 / Χ2: 0.99 / Net I/σ(I): 17 / Num. measured all: 482366
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 25.5 % / Rmerge(I) obs: 2.994 / Num. measured all: 57466 / Num. unique obs: 2255 / CC1/2: 0.771 / Rpim(I) all: 0.601 / Rrim(I) all: 3.055 / Χ2: 0.97 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→34.25 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 988 4.89 %
Rwork0.198 --
obs0.1998 20222 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 3 14 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062999
X-RAY DIFFRACTIONf_angle_d0.5564042
X-RAY DIFFRACTIONf_dihedral_angle_d13.3211121
X-RAY DIFFRACTIONf_chiral_restr0.045478
X-RAY DIFFRACTIONf_plane_restr0.006508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.38321330.34832704X-RAY DIFFRACTION100
2.63-2.80.30811390.26412693X-RAY DIFFRACTION100
2.8-3.010.2951380.25322704X-RAY DIFFRACTION100
3.01-3.320.27591540.23522704X-RAY DIFFRACTION100
3.32-3.790.29211320.21562753X-RAY DIFFRACTION100
3.79-4.780.18381460.16742771X-RAY DIFFRACTION100
4.78-34.250.20991460.16962905X-RAY DIFFRACTION99
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)
15.809-0.6407-0.51754.94910.66985.4189-0.01-1.0273-1.39750.0553-0.1383-0.22580.33810.19880.16560.57320.0170.16930.73880.25171.0793-16.4765-36.51919.4544
26.76845.91495.53776.56095.13954.59360.1013-0.58370.47060.498-0.76570.38710.4416-0.18110.46010.6504-0.03030.06930.72050.15180.9809-6.2299-29.37360.6606
35.1794-1.1377-2.43161.3306-0.41673.3928-0.0942-0.4436-0.49850.1941-0.0930.0423-0.07560.15630.17940.562-0.04770.0160.56550.0480.765-15.4456-23.91031.2851
48.85672.84711.6834.72165.62969.1407-0.1198-0.1228-1.67251.2825-0.21321.88471.1561-0.6920.21220.6951-0.04740.12870.57770.06961.2696-29.233-34.18812.3366
58.06781.619-0.50667.0457-0.15775.7645-0.4777-0.37970.74140.4380.0932-0.8629-0.14970.29320.34590.54790.0107-0.19550.61460.13781.104218.0812-5.41529.1332
65.6856-1.9071-5.61571.87031.78125.5811-0.821-0.9997-0.12690.5937-0.4611-0.6705-0.75970.91841.15240.7590.0382-0.22890.82030.08931.1836.53822.43483.2661
72.3417-3.31341.84534.7368-2.7513.9448-0.19360.20290.584-0.0935-0.0635-0.5205-0.0276-0.27380.24970.5589-0.0296-0.02380.6780.11630.91066.2123-7.97740.4596
86.25710.0826-4.91547.013-0.01094.02130.1018-0.3549-1.26910.0528-0.8427-1.9786-0.41621.35610.72440.6438-0.0307-0.04270.95130.32951.197321.8328-15.0326-1.9125
97.43710.0528-0.37915.1863-1.61664.95890.6123-0.54461.1528-0.2706-0.29451.22830.031-1.18730.13960.65560.0771-0.14650.8419-0.2590.6274-27.70219.02778.9534
104.3857-0.4716-0.47395.97720.7154.57690.0701-0.60880.38930.5294-0.14160.0373-0.0939-0.08780.06950.8393-0.0155-0.03660.8165-0.17890.7755-25.00797.107618.0513
117.27941.0214-3.28324.6244-4.43455.0885-0.37710.08640.21060.2772-0.05910.57950.3123-0.15750.58580.6883-0.0411-0.14450.6071-0.08220.9845-28.4894-0.60084.2279
122.20561.73980.55642.25950.95132.0275-0.0772-0.31150.16940.0264-0.06720.50490.1961-0.27260.11390.66920.026-0.09840.6369-0.11040.6839-18.23952.56885.2766
133.0855-4.7110.50777.9189-2.75817.7255-0.2324-1.06811.73970.17190.2520.3016-0.9676-0.3668-0.04520.91980.0736-0.27450.7852-0.18881.2372-19.784119.45888.4312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 126 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 54 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 71 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 110 )
8X-RAY DIFFRACTION8chain 'B' and (resid 111 through 126 )
9X-RAY DIFFRACTION9chain 'C' and (resid 0 through 10 )
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 60 )
11X-RAY DIFFRACTION11chain 'C' and (resid 61 through 71 )
12X-RAY DIFFRACTION12chain 'C' and (resid 72 through 110 )
13X-RAY DIFFRACTION13chain 'C' and (resid 111 through 126 )

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