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- PDB-1s89: H98N Mutant of Methylglyoxal Synthase from E. coli complexed with... -

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Basic information

Entry
Database: PDB / ID: 1s89
TitleH98N Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid
ComponentsMethylglyoxal synthase
KeywordsLYASE / GLYCOLYTIC BYPASS / METHYLGLYOXAL
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / protein hexamerization / identical protein binding / 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
2-PHOSPHOGLYCOLIC ACID / Methylglyoxal synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMarks, G.T. / Harrison, D.H. / Susler, M.
CitationJournal: Biochemistry / Year: 2004
Title: Mutagenic studies on histidine 98 of methylglyoxal synthase: effects on mechanism and conformational change.
Authors: Marks, G.T. / Susler, M. / Harrison, D.H.
History
DepositionJan 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
D: Methylglyoxal synthase
E: Methylglyoxal synthase
F: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,41712
Polymers101,4816
Non-polymers9366
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20140 Å2
ΔGint-168 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.479, 129.497, 178.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Methylglyoxal synthase / MGS


Mass: 16913.500 Da / Num. of mol.: 6 / Mutation: H98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MGSA, B0963, Z1314, ECS1047, SF0965, S1031 / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / Strain (production host): ML1 / References: UniProt: P0A731, methylglyoxal synthase
#2: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 1500, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 9, 2002
RadiationMonochromator: Osmic Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→29.24 Å / Num. obs: 60966 / Observed criterion σ(F): 0 / Biso Wilson estimate: 11.6 Å2 / Limit h max: 23 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 79 / Limit l min: 0 / Observed criterion F max: 120436.53 / Observed criterion F min: 0.172
Reflection shellResolution: 2.2→2.24 Å

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→29.24 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3795 7.5 %shells
Rwork0.19 ---
all-62179 --
obs-50265 80.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 26.6625 Å2 / ksol: 0.298543 e/Å3
Displacement parametersBiso max: 64.18 Å2 / Biso mean: 27.32 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-7.63 Å20 Å20 Å2
2---1.6 Å20 Å2
3----6.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Luzzati d res high-2.22
Refinement stepCycle: LAST / Resolution: 2.22→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 54 129 7211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.4
X-RAY DIFFRACTIONx_torsion_impr_deg3.19
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.22-2.320.2682533.30.26740140.0177683426755.5
2.32-2.440.2415066.60.24153190.0117676582575.9
2.44-2.60.2315066.60.23154460.017671595277.6
2.6-2.80.2285066.60.22857780.017720628481.4
2.8-3.080.2125066.60.21361120.0097706661885.9
3.08-3.520.1975066.50.19764920.0097776699890
3.52-4.430.1575066.40.15566440.0077862715090.9
4.43-29.240.1535066.20.15566650.0078128717188.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3TOPPAR2:pga.parTOPPAR2:pga.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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