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- PDB-2xw6: The Crystal Structure of Methylglyoxal Synthase from Thermus sp. ... -

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Basic information

Entry
Database: PDB / ID: 2xw6
TitleThe Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Phosphate Ion.
ComponentsMETHYLGLYOXAL SYNTHASE
KeywordsLYASE
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
PHOSPHATE ION / Methylglyoxal synthase
Similarity search - Component
Biological speciesTHERMUS SP. GH5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsShahsavar, A. / Erfani Moghaddam, M. / Antonyuk, S.V. / Khajeh, K. / Naderi-Manesh, H.
CitationJournal: To be Published
Title: Atomic Resolution Structure of Methylglyoxal Synthase from Thermus Sp. Gh5 Bound to Phosphate: Insights Into the Distinctive Effects of Phosphate on the Enzyme Structure
Authors: Shahsavar, A. / Erfani Moghaddam, M. / Antonyuk, S.V. / Khajeh, K. / Naderi-Manesh, H.
History
DepositionNov 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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)44,0516
Polymers43,7673
Non-polymers2853
Water8,341463
1
A: METHYLGLYOXAL SYNTHASE
B: METHYLGLYOXAL SYNTHASE
C: METHYLGLYOXAL SYNTHASE
hetero molecules

A: METHYLGLYOXAL SYNTHASE
B: METHYLGLYOXAL SYNTHASE
C: METHYLGLYOXAL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,10312
Polymers87,5336
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area13170 Å2
ΔGint-113.8 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.636, 115.172, 120.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2137-

HOH

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Components

#1: Protein METHYLGLYOXAL SYNTHASE / MGS


Mass: 14588.838 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS SP. GH5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B3VH91, methylglyoxal synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.16 Å3/Da / Density % sol: 43.07 % / Description: NONE
Crystal growTemperature: 277 K / Method: microbatch / pH: 8
Details: CRYSTALS WERE OBTAINED USING MICROBATCH METHOD AT 4C. CRYSTALLIZATION DROPS WERE MADE BY MIXING 2 MICROLITER OF A 7.8 MG/ML PROTEIN SOLUTION IN 50 MM TRIS-HCL, 300 MM NACL, 160 MM IMIDAZOLE ...Details: CRYSTALS WERE OBTAINED USING MICROBATCH METHOD AT 4C. CRYSTALLIZATION DROPS WERE MADE BY MIXING 2 MICROLITER OF A 7.8 MG/ML PROTEIN SOLUTION IN 50 MM TRIS-HCL, 300 MM NACL, 160 MM IMIDAZOLE AND 20% GLYCEROL WITH EQUAL AMOUNT OF CRYSTALLIZATION SOLUTION CONTAINING 0.1 M TRIS-HCL (PH 8.0), 29% W/V POLYETHYLENE GLYCOL (PEG) 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 25, 2009 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.08→42.2 Å / Num. obs: 156269 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.8 / % possible all: 81.1

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WO8

1wo8


Resolution: 1.08→42.2 Å / Num. parameters: 33060 / Num. restraintsaints: 43564 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.161 7806 5.3 %RANDOM
all0.129 148053 --
obs0.129 -96.6 %-
Refine analyzeNum. disordered residues: 58 / Occupancy sum hydrogen: 2925.64 / Occupancy sum non hydrogen: 3293.85
Refinement stepCycle: LAST / Resolution: 1.08→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 15 463 3381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.083
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.109

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