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- PDB-3t0c: Crystal structure of Streptococcus mutans MetE complexed with Zinc -

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Basic information

Entry
Database: PDB / ID: 3t0c
TitleCrystal structure of Streptococcus mutans MetE complexed with Zinc
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / MetE / Barrel / methyltransferase
Function / homology
Function and homology information


5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / 'de novo' L-methionine biosynthetic process / methylation / zinc ion binding
Similarity search - Function
Cobalamin-independent methionine synthase / Cobalamin-independent methionine synthase MetE, N-terminal / Cobalamin-independent synthase, N-terminal domain / Cobalamin-independent methionine synthase MetE, C-terminal/archaeal / Cobalamin-independent synthase, Catalytic domain / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.187 Å
AuthorsFu, T.M. / Liang, Y.H. / Su, X.D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structures of Cobalamin-Independent Methionine Synthase (MetE) from Streptococcus mutans: A Dynamic Zinc-Inversion Model
Authors: Fu, T.M. / Almqvist, J. / Liang, Y.H. / Li, L. / Huang, Y. / Su, X.D.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 3, 2011ID: 3L7S
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1535
Polymers87,8001
Non-polymers3544
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.845, 99.477, 77.883
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Cobalamin-independent methionine synthase / Methionine synthase / vitamin-B12 independent isozyme


Mass: 87799.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: metE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8CWX6, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Li2SO4, 0.1M HEPES, 25%(w/v) polyethylene glycerol 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.187→52.63 Å / Num. all: 40832 / Num. obs: 39151 / % possible obs: 95.88 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.31 % / Biso Wilson estimate: 20.74 Å2
Reflection shellResolution: 2.19→2.33 Å / Num. unique all: 6372 / % possible all: 77.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NQ5

2nq5


Resolution: 2.187→42.068 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.7848 / SU ML: 0.35 / σ(F): 1.91 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1948 4.98 %
Rwork0.2095 --
obs0.2119 39089 47.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.393 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 70.47 Å2 / Biso mean: 26.1002 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1--6.1795 Å2-0 Å21.3858 Å2
2---8.0329 Å2-0 Å2
3---14.2124 Å2
Refinement stepCycle: LAST / Resolution: 2.187→42.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5599 0 16 493 6108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035731
X-RAY DIFFRACTIONf_angle_d0.6687818
X-RAY DIFFRACTIONf_chiral_restr0.046908
X-RAY DIFFRACTIONf_plane_restr0.0031010
X-RAY DIFFRACTIONf_dihedral_angle_d15.2071978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1865-2.24120.2898620.2291640170229
2.2412-2.30180.2581070.22652209231639
2.3018-2.36950.28781290.21772455258445
2.3695-2.4460.30751600.21482764292450
2.446-2.53340.27811590.21082797295651
2.5334-2.63480.26761460.21292839298551
2.6348-2.75470.27031270.21252799292651
2.7547-2.89990.26861640.21742794295851
2.8999-3.08150.27341460.22082814296051
3.0815-3.31940.25511390.21182841298051
3.3194-3.65330.28071490.19992782293151
3.6533-4.18150.20731450.18192806295151
4.1815-5.26660.21741690.18472808297751
5.2666-42.07530.24741460.2352793293950

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