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- PDB-3bq5: Crystal Structure of T. maritima Cobalamin-Independent Methionine... -

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Basic information

Entry
Database: PDB / ID: 3bq5
TitleCrystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)
Components5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
KeywordsTRANSFERASE / MetE / TIM BARREL / HOMOCYSTEINE / ZINC / ZINC INVERSION / Amino-acid biosynthesis / Metal-binding / Methionine biosynthesis / 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
2-AMINO-4-MERCAPTO-BUTYRIC ACID / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPejchal, R. / Smith, J.L. / Ludwig, M.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Metal active site elasticity linked to activation of homocysteine in methionine synthases.
Authors: Koutmos, M. / Pejchal, R. / Bomer, T.M. / Matthews, R.G. / Smith, J.L. / Ludwig, M.L.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
B: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,3468
Polymers178,8212
Non-polymers5256
Water7,530418
1
A: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6734
Polymers89,4101
Non-polymers2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6734
Polymers89,4101
Non-polymers2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.229, 107.164, 107.667
Angle α, β, γ (deg.)90.00, 108.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 89410.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: metE / Plasmid: pET-151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3)
References: UniProt: Q9X112, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 295 K / Method: vapor batch, under oil / pH: 8.5
Details: 19.5% PEG 3350, 0.2M magnesium acetate, 2.5% ethylene glycol, 0.1M Tris-HCl, pH 8.5, VAPOR BATCH, UNDER OIL, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2006
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→47.4 Å / Num. all: 104606 / Num. obs: 104398 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 34.7 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 15374 / Rsym value: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T7L

1t7l


Resolution: 2→47.4 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 2610 2.5 %RANDOM
Rwork0.217 ---
obs0.218 104398 99.8 %-
all-104606 --
Displacement parametersBiso mean: 38.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.903 Å20 Å25.615 Å2
2---4.632 Å20 Å2
3---2.729 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11230 0 26 418 11674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfOND0.005
X-RAY DIFFRACTIONfNGLE0.851
X-RAY DIFFRACTIONfHIRALITY0.061
X-RAY DIFFRACTIONfLANARITY0.004
X-RAY DIFFRACTIONfIHEDRAL16.341
LS refinement shellResolution: 2→2.047 Å
RfactorNum. reflection% reflection
Rfree0.301 136 -
Rwork0.276 --
obs-5470 100 %

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