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- PDB-2ogy: Asn199Ala Mutant of the 5-methyltetrahydrofolate corrinoid/iron s... -

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Basic information

Entry
Database: PDB / ID: 2ogy
TitleAsn199Ala Mutant of the 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase complexed with methyltetrahydrofolate to 2.3 Angstrom 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 / 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-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: 2.3 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. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)58,1896
Polymers57,1902
Non-polymers9994
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-43 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.772, 78.673, 135.857
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: 28595.096 Da / Num. of mol.: 2 / Mutation: N199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: 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.: 322 / 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: 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: X25 / Wavelength: 0.91938
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 2002
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: 2.3→46.73 Å / Num. obs: 24151 / % possible obs: 99.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1752 / Rsym value: 0.385 / % possible all: 99.3

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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: 2.3→40.19 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: REFMAC was also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.23408 2369 -RANDOM
Rwork0.18271 ---
obs0.18767 21756 98.68 %-
all-24125 --
Refinement stepCycle: LAST / Resolution: 2.3→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 68 322 4378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.995
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection% reflection
Rfree0.238 158 -
Rwork0.198 --
obs-1588 99.15 %

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