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- PDB-2e7f: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltran... -

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Basic information

Entry
Database: PDB / ID: 2e7f
Title5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase complexed with methyltetrahydrofolate to 2.2 Angsrom resolution
Components5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
KeywordsTRANSFERASE / Methyltetrahydrofolate-protein complex / corrionoid / vitamin B12 / TIM Barrel
Function / homology
Function and homology information


5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / pteridine-containing compound metabolic process / methionine synthase activity / carbon fixation / cobalamin binding / 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-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein co-methyltransferase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDoukov, T.I. / Drennan, C.L. / Hemmi, H. / Ragsdale, S.W.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases.
Authors: Doukov, T.I. / Hemmi, H. / Drennan, C.L. / Ragsdale, S.W.
#1: Journal: Structure / Year: 2000
Title: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase
Authors: Doukov, T.I. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
History
DepositionJan 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
B: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2756
Polymers57,2762
Non-polymers9994
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-43 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.159, 78.547, 135.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S)

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Components

#1: Protein 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase


Mass: 28638.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: MeTr, acsE / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS(met-) / References: UniProt: Q46389
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-15% PEGmme 5000, 0.05M Calcium acetate, 20% Glycerol, 0.05M HEPES buffer; 3-fold molar excess of the MTHF substrate (Schricks Labolatories, Jona, Switzerland). The supersaturation of the ...Details: 8-15% PEGmme 5000, 0.05M Calcium acetate, 20% Glycerol, 0.05M HEPES buffer; 3-fold molar excess of the MTHF substrate (Schricks Labolatories, Jona, Switzerland). The supersaturation of the precipitant solution required dilution of the protein-CH3-H4folate complex by 50-100-fold in order to obtain single crystals., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91938 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 30, 2000
RadiationMonochromator: SI(111) or SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91938 Å / Relative weight: 1
ReflectionResolution: 2.2→30.92 Å / Num. obs: 26806 / % possible obs: 96.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1750 / Rsym value: 0.206 / % possible all: 87.9

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Processing

Software
NameVersionClassification
CBASSdata collection
EPMRphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F6Y

1f6y


Resolution: 2.2→30.88 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2586 -RANDOM
Rwork0.172 ---
obs0.178 24177 96.04 %-
all-26763 --
Refinement stepCycle: LAST / Resolution: 2.2→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 68 435 4497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.018
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.245 165 -
Rwork0.193 --
obs-1571 85.77 %

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