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- PDB-2zvi: Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate en... -

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Basic information

Entry
Database: PDB / ID: 2zvi
TitleCrystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis
Components2,3-diketo-5-methylthiopentyl-1-phosphate enolase
KeywordsISOMERASE / ENOLASE / METHIONINE SALVAGE PATHWAY / Amino-acid biosynthesis / Magnesium / Metal-binding / Methionine biosynthesis
Function / homology
Function and homology information


2,3-diketo-5-methylthiopentyl-1-phosphate enolase / 2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / ribulose-bisphosphate carboxylase activity / magnesium ion binding
Similarity search - Function
2,3-diketo-5-methylthiopentyl-1-phosphate enolase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain ...2,3-diketo-5-methylthiopentyl-1-phosphate enolase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-diketo-5-methylthiopentyl-1-phosphate enolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTamura, H. / Yadani, T. / Kai, Y. / Inoue, T. / Matsumura, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis
Authors: Tamura, H. / Saito, Y. / Ashida, H. / Kai, Y. / Inoue, T. / Yokota, A. / Matsumura, H.
History
DepositionNov 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
B: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
C: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
D: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase


Theoretical massNumber of molelcules
Total (without water)185,0714
Polymers185,0714
Non-polymers00
Water5,549308
1
A: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
B: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase


Theoretical massNumber of molelcules
Total (without water)92,5362
Polymers92,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-29 kcal/mol
Surface area28240 Å2
MethodPISA
2
C: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
D: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase


Theoretical massNumber of molelcules
Total (without water)92,5362
Polymers92,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-31 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.334, 91.466, 106.967
Angle α, β, γ (deg.)90.00, 90.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
2,3-diketo-5-methylthiopentyl-1-phosphate enolase / / DK-MTP-1-P enolase


Mass: 46267.785 Da / Num. of mol.: 4 / Fragment: Residues 10-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O31666, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.14M Na Thiocyanate, 21% (w/v) polyethylene glycol 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30.5 Å / Num. obs: 64719 / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.273

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OEK

2oek


Resolution: 2.3→30.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1983182.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3267 5 %RANDOM
Rwork0.201 ---
obs0.201 64711 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.5652 Å2 / ksol: 0.358204 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å22.45 Å2
2--8.46 Å20 Å2
3----4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11945 0 0 308 12253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 516 4.8 %
Rwork0.24 10262 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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