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- PDB-1wo8: Crystal structure of methylglyoxal synthase from Thermus thermoph... -

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Basic information

Entry
Database: PDB / ID: 1wo8
TitleCrystal structure of methylglyoxal synthase from Thermus thermophilus HB8
Componentsmethylglyoxal synthase
KeywordsLYASE / methylglyoxal synthase / Thermus thermophilus HB8 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
Methylglyoxal synthase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8
Authors: Sugahara, M. / Kunishima, N.
History
DepositionAug 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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)81,05913
Polymers80,3866
Non-polymers6727
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-199 kcal/mol
Surface area25560 Å2
MethodPISA
2
A: methylglyoxal synthase
B: methylglyoxal synthase
C: methylglyoxal synthase
D: methylglyoxal synthase
E: methylglyoxal synthase
F: methylglyoxal synthase
hetero molecules

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)162,11826
Polymers160,77312
Non-polymers1,34514
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area28930 Å2
ΔGint-410 kcal/mol
Surface area48450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.612, 130.612, 96.653
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-1101-

HOH

21C-1102-

HOH

31E-1121-

HOH

DetailsThe biological assembly is a hexamer(chain A,B,C,D,E,F) in the asymmetric unit.

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Components

#1: Protein
methylglyoxal synthase


Mass: 13397.733 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHD6, methylglyoxal synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / 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 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: Lithium sulfate, pH 4.6, microbatch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
ROTATING ANODERIGAKU21.54178
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS V1IMAGE PLATEJul 7, 2004
RIGAKU RAXIS IV2IMAGE PLATEJul 27, 2004mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541781
ReflectionResolution: 1.7→40 Å / Num. all: 104491 / Num. obs: 104491 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 19.44 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.1 / Net I/σ(I): 6.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.1 / Num. unique all: 10286 / Rsym value: 0.405 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.1 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5144 -RANDOM
Rwork0.185 ---
all0.186 104336 --
obs0.186 104336 99.9 %-
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.25 Å20 Å2
2---1.14 Å20 Å2
3---2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 35 816 6357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.268 510 -
Rwork0.234 --
obs-9817 99.9 %

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