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- PDB-1f6y: MAD CRYSTAL STRUCTURE ANALYSIS OF METHYLTETRAHYDROFOLATE: CORRINO... -

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Basic information

Entry
Database: PDB / ID: 1f6y
TitleMAD CRYSTAL STRUCTURE ANALYSIS OF METHYLTETRAHYDROFOLATE: CORRINOID/IRON-SULFUR PROTEIN METHYLTRANSFERASE (METR)
Components5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
KeywordsTRANSFERASE / carbon dioxide fixation / cobalamin / methyltatrahydrofolate / methyltransferase / one-carbon metabolism / TIM barrel / homodimer
Function / homology
Function and homology information


5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / methionine synthase activity / homocysteine metabolic process / carbon fixation / cobalamin binding / tetrahydrofolate metabolic process / methyltransferase activity / methylation / calcium ion binding / cytosol
Similarity search - Function
: / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-methyltetrahydrofolate:corrinoid/iron-sulfur protein co-methyltransferase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 2.2 Å
AuthorsDoukov, T.I. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase.
Authors: Doukov, T. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Preliminary X-ray Crystallographic Study of Methyltetrahydrofolate: Corrinoid/Iron-Sulfur Protein Methyltransferase from Clostridium thermoaceticum
Authors: Doukov, T.I. / Zhao, S. / Ross II, C.R. / Roberts, D.L. / Kim, J.J. / Ragsdale, S.W. / Stezowski, J.J.
#2: Journal: J.BACTERIOL. / Year: 1994
Title: The Reductive Acetyl Coenzyme A Pathway: Sequence and Heterologous Expression of Active Methyltetrahydrofolate:Corrinoid/Iron-Sulfur Protein Methyltransferase from Clostridium thermoaceticum
Authors: Roberts, D.L. / Zhao, S. / Doukov, T. / Ragsdale, S.W.
#3: Journal: Biochemistry / Year: 1999
Title: Binding of (6R,S)-Methyltetrahydrofolate to Methyltransferase from Clostridium thermoaceticum: Role of Protonation of Methyltetrahydrofolate in the Mechanism of Methyl Transfer
Authors: Seravalli, J. / Shoemaker, R.K. / Sudbeck, M.L. / Ragsdale, S.W.
#4: Journal: Biochemistry / Year: 1999
Title: Mechanism of Transfer of the Methyl Group from (6S)-Methyltetrahydrofolate to the Corrinoid/Iron-Sulfur Protein Catalyzed by the Methyltransferase from Clostridium thermoaceticum: A Key Step ...Title: Mechanism of Transfer of the Methyl Group from (6S)-Methyltetrahydrofolate to the Corrinoid/Iron-Sulfur Protein Catalyzed by the Methyltransferase from Clostridium thermoaceticum: A Key Step in the Wood-Ljungdahl Pathway of Acetyl-CoA Synthesis
Authors: Seravalli, J. / Zhao, S. / Ragsdale, S.W.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
B: 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)57,3402
Polymers57,3402
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 89.412, 115.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE


Mass: 28670.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Strain: ATCC 39073 / Cellular location: CYTOPLASMIC / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q46389
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9-15% PEGmme 5000, 20% Glycerol, 50 mM HEPES pH 7.5, 20-50 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
pH: 7.6 / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMdithiothreitol1drop
250 mMTris1drop
310 mM1dropNaCl
420 mg/mlprotein1drop
59-15 %(w/v)PEGmme50001reservoir
620-50 mM1reservoirCaCl2
720 %glycerol1reservoir
850 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→7 Å / Num. all: 34455 / Num. obs: 28189 / % possible obs: 81.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.7
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.294 / % possible all: 87.6

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 2.2→7 Å / Num. parameters: 1650 / Num. restraintsaints: 1601 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 291 10 %Thin sliced (SHELX97)
Rwork0.2012 ---
all0.209 34455 --
obs0.206 28189 81.8 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4125
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 0 185 4125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.01
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.2306 / Rfactor Rwork: 0.2064
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_plane_restr0.031

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