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- PDB-5h3l: Structure of methylglyoxal synthase crystallised as a contaminant -

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Basic information

Entry
Database: PDB / ID: 5h3l
TitleStructure of methylglyoxal synthase crystallised as a contaminant
ComponentsMethylglyoxal synthase
KeywordsLYASE / Contaminant
Function / homologyMethylglyoxal synthase-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHatti, K. / Dadireddy, V. / Srinivasan, N. / Ramakumar, S. / Murthy, M.R.N.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structure determination of contaminant proteins using the MarathonMR procedure.
Authors: Hatti, K. / Biswas, A. / Chaudhary, S. / Dadireddy, V. / Sekar, K. / Srinivasan, N. / Murthy, M.R.
History
DepositionOct 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)51,0146
Polymers50,8763
Non-polymers1383
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.500, 86.500, 132.100
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: 16958.518 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5M Sodium formate.HCl, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.1→61.16 Å / Num. all: 30046 / Num. obs: 29980 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.991 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 14.6 % / Rmerge(I) obs: 2.179 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.436 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B93

1b93


Resolution: 2.1→61.165 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35
RfactorNum. reflection% reflection
Rfree0.2518 1501 5.01 %
Rwork0.1952 --
obs0.198 29977 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→61.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 9 125 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083514
X-RAY DIFFRACTIONf_angle_d0.8724794
X-RAY DIFFRACTIONf_dihedral_angle_d12.3822098
X-RAY DIFFRACTIONf_chiral_restr0.056564
X-RAY DIFFRACTIONf_plane_restr0.006617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.36421560.30422518X-RAY DIFFRACTION100
2.1678-2.24530.34331260.25832535X-RAY DIFFRACTION100
2.2453-2.33520.32421540.26092534X-RAY DIFFRACTION100
2.3352-2.44150.24261240.2252536X-RAY DIFFRACTION100
2.4415-2.57020.28541410.21732554X-RAY DIFFRACTION100
2.5702-2.73130.28831540.21492543X-RAY DIFFRACTION100
2.7313-2.94210.25691290.20742575X-RAY DIFFRACTION100
2.9421-3.23820.261370.20572582X-RAY DIFFRACTION100
3.2382-3.70670.25771370.17552619X-RAY DIFFRACTION100
3.7067-4.66980.16721330.13772640X-RAY DIFFRACTION100
4.6698-61.19050.20311100.16952840X-RAY DIFFRACTION100

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