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- PDB-1egh: STRUCTURE OF METHYLGLYOXAL SYNTHASE COMPLEXED WITH THE COMPETITIV... -

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Basic information

Entry
Database: PDB / ID: 1egh
TitleSTRUCTURE OF METHYLGLYOXAL SYNTHASE COMPLEXED WITH THE COMPETITIVE INHIBITOR 2-PHOSPHOGLYCOLATE
ComponentsMETHYLGLYOXAL SYNTHASE
KeywordsLYASE / beta/alpha protein
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 / Resolution: 2 Å
AuthorsSaadat, D. / Harrison, D.H.T.
CitationJournal: Biochemistry / Year: 2000
Title: Mirroring perfection: the structure of methylglyoxal synthase complexed with the competitive inhibitor 2-phosphoglycolate.
Authors: Saadat, D. / Harrison, D.H.
History
DepositionFeb 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)102,56112
Polymers101,6256
Non-polymers9366
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19990 Å2
ΔGint-183 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.12, 129.87, 178.55
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is contained within the assymetric unit as a homohexamer composed of chains A,B,C,D,E,F

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Components

#1: Protein
METHYLGLYOXAL SYNTHASE


Mass: 16937.545 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / 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.: 300 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 1500, sodium cacodylate, imidazole-HCL, potassium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG15001reservoir
2100 mMsodium cacodylate1reservoir
325 mg/mlprotein1drop
420 mMimidazole-HCl1drop
51 mMpotassium phosphate1drop
610 mM2-phosphoglycolate1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 75167 / Num. obs: 74966 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.287 / Num. unique all: 2654 / % possible all: 63.7
Reflection
*PLUS
Num. measured all: 166553 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 63.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3439 5 %SHELLS
Rwork0.187 ---
obs0.187 68596 81.2 %-
all-74777 --
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 0 54 300 7322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_improper_angle_d0.63
X-RAY DIFFRACTIONx_mcbond_it2.111.5
X-RAY DIFFRACTIONx_mcangle_it3.242
X-RAY DIFFRACTIONx_scbond_it42
X-RAY DIFFRACTIONx_scangle_it6.12.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 393 5.1 %
Rwork0.274 7239 -
obs--54.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PGA.PARTOPH19.SOL
X-RAY DIFFRACTION3PGA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.63
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.274 / Rfactor obs: 0.279

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